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Genetic resources are important for the development of every country and for humanity. Collection, conservation and reasonable utilization of genetic resource is required mission. Understanding the importance of genetic resource, especially rice germplasm, since 2001, Center for conservation and development of crop genetic resources (CCD-CGR) of Hanoi University of Agriculture (Vietnam National University of Agriculture) has been collected, conserved and evaluated rice germplasm from different provinces of Vietnam for breeding programs. So far, 1090 accessions of local rice of Vietnam have been collected. Evaluation of agronomic properties and screening of some important genes using DNA molecular markers have revealed that Vietnamese rice germplasm has high level diversity and containing important genes for quality and resistance for disease and pests. These genetic resources are potential materials for national breeding programs. Based on the collected germplasm, 3 new glutinous rice varieties have been successfully created with high yield and good quality. In addition, the degradation of local rice varieties is also a matter of concern. So far, 4 specialty rice varieties Deo Dang, Ble chau, Pu de and Khau dao have been successfully restored for the north provinces of Vietnam. The main results of this study are germplasms for rice breeding programs and new improved varieties that bring economic benefits to farmers and the country. / Nguồn gene là tài nguyên sống còn của mỗi quốc gia và của toàn nhân loại. Vì vậy thu thập, bảo tồn, đánh giá và khai thác hợp lý nguồn tài nguyên này có ý nghĩa rất lớn. Nhận thức được tầm quan trọng của nguồn gen nhất là nguồn gen cây lúa, ngay từ đầu những năm 2000, Trung tâm bảo tồn và phát triển nguồn gene cây trồng thuộc Trường Đại học nông nghiệp, nay là Học Viện nông nghiệp Việt Nam đã tiến hành thu thập, lưu giữ, đánh giá và khai thác nguồn gene lúa. Kết quả đã thu thập, lưu giữ được 1090 mẫu giống lúa địa phương Việt Nam. Đánh giá đặc điểm nông sinh học và phát hiện một số gene quy định các tính trạng chất lượng và kháng sâu bệnh bằng chỉ thị phân tử DNA. Đây là nguồn gene quan trọng cho chọn tạo giống. Dựa vào nguồn gene thu thập được, cho đến nay, Trung tâm bảo tồn và phát triển nguồn gene cây trồng đã lai và chọn tạo được thành công 03 giống lúa nếp chất lượng cao. Ngoài ra, thoái hóa giống cũng là vấn đề đang được quan tâm. Cho đến nay 4 giống lúa đặc sản Đèo đàng, Ble châu, Pu đe và Khẩu dao đã được phục tráng và đưa vào sản xuất. Kết quả của những nghiên cứu này là ngân hàng các giống lúa làm nguồn gene để chọn tạo giống mới đem lại lợi ích kinh tế cho người nông dân và đất nước.

Rice (Oryza sativa L.) is the second most important cereal crop in Malawi. Rice productivity in the dominant (85%) rainfed ecosystem is very low, with mean yield of only 1.4 t ha-1. Farmers plant traditional landraces that have low yield potential and are susceptible to various stresses such as drought and diseases. Development and introduction of improved rice varieties, with stress tolerance traits from introduced varieties, such as the New Rice for Africa (NERICAs), could significantly increase productivity. Previous attempts to introduce high yielding irrigated varieties into the dominant rainfed ecosystem in Malawi have not been successful because farmers basically did not adopt the varieties, claiming that the varieties were lacking in grain traits that they preferred but that the traits were present in their landraces. The notable traits mentioned, through previous informal surveys, were long grains, medium to slender shape and aromatic grain with intermediate gelatinization temperature. No formal study has been conducted to ascertain the preferences, and the genetic control of the traits, including yield and yield related traits, have not been studied. The objectives of this study were to: 1) confirm farmers’ preferences for grain traits using participatory rural appraisal; 2) determine amount of genetic variability for yield and yield related traits in Malawi rice landraces, 3) determine the genetic control and correlations of grain length, grain shape and 1000-grain weight, 4) determine the inheritance of aroma and gelatinization temperature and, 5) determine the genetic control, correlations and path coefficients of yield and yield related traits, in F2 generations of Malawi rice landraces and NERICA varieties crosses. To confirm the farmers’ preferences for grain traits, a participatory rural appraisal was conducted in 2006 in two villages that were representative of rainfed rice growing areas in Malawi. The villages were Liundi and Nawanga in Machinga and Salima Districts, respectively. Qualitative and quantitative data were collected through questionnaires and discussions with 190 respondents, as well as through observations. To determine variability among Malawi rice landraces, 19 landraces were planted at Lifuwu in a Randomized Complete Block Design with three replicates in 2006. Data on plant height, days to 50% flowering, number of panicles per hill, panicle length, number of filled grains per panicle, 1000-grain weight, panicle weight, grain length and grain yield were collected and analyzed. Four Malawi rice landraces were crossed to four NERICA varieties in 2006 in a North Carolina Design II mating scheme to determine the genetic control of grain size. F1 plants were raised in 2007 and in 2008, 16 F2 populations together with their parents were planted in a Randomized Complete Block Design with three replicates at Lifuwu. Data on grain length, grain shape and 1000-grain weight were collected and analyzed. To determine the inheritance of aroma and gelatinization temperature, four Malawi rice landraces were crossed to four NERICA varieties in 2006 and F1 plants were raised in 2007. In 2008, 16 F2 populations together with their parents were planted in a Randomized Complete Block Design with three replicates at Lifuwu. Aroma and gelatinization temperature were evaluated. To determine the gene action of yield and yield related traits, four Malawi rice landraces were crossed to four NERICA varieties in 2006 in a North Carolina Design II mating scheme and F1 plants were raised in 2007. In 2008, 16 F2 populations together with their parents were planted in a Randomized Complete Block Design with three replicates at Lifuwu. Data on grain yield, the number of panicles per hill, days to 50% flowering, panicle length, panicle weight and 1000-grain weight were collected and analyzed The participatory rural appraisal confirmed that that long, slender or medium shape grains, with aroma and intermediate gelatinization temperature were the key traits preferred by farmers. Therefore the farmer preferred traits of long, slender grains, with aroma and medium gelatinization temperature, must be selected for in any high yielding varieties to be developed for the rainfed rice ecosystem. Results showed that differences were significant (P=0.05) for all the traits that were studied. Heritability estimates were low to moderate: 18.3% for panicle weight, 40.0% for panicles per hill and 56.3% for days to 50% flowering date. The high genetic variability among the landraces could be used in a breeding programme to develop improved varieties for various morphological traits. The number of panicles per hill and 1000-grain weight combined moderate heritabilities with relatively high genetic advance and therefore could be reliable traits for yield improvement. Genetic analysis of grain size showed that Malawi rice landraces were variable for all three grain size characteristics, namely grain length, grain shape and 1000-grain weight. NERICA varieties were variable for 1000-grain weight. Sixteen F2 progenies were variable for all three characteristics, and the variability was significant (P=0.05). Heritability estimates were high (45.4%) for grain length and low for grain shape (12.3%) and for 1000-grain weight (14.3%) suggesting that early generation selection would be effective for grain length. Predominance of additive gene action for grain length and grain shape suggested that early generation selection would be effective for these traits. Selection for 1000-grain weight would be more effective in later generations because of preponderance of non-additive gene action in the control of this trait. The correlation between grain length and grain shape was positive (r=0.769) and highly significant (P=0.01) suggesting that breeders would choose to select for both traits simultaneously, or they would choose one of the traits to develop varieties with long grains and medium shape. Crosses between aromatic and non-aromatic varieties had non-aromatic F1. The F2 progenies segregated into 3:1 ratio for non-aromatic: aromatic suggesting that, in the Malawi rice landraces, aroma was probably simply inherited through a single recessive gene. F1 progenies, between parents with high and intermediate gelatinization temperatures had intermediate gelatinization temperature. F2 progenies segregated into 1:3 ratios for high; intermediate gelatinization temperature in three out of four crosses suggesting control by one dominant gene. The segregation pattern in one cross was not significantly different from 3:13 ratio for high: intermediate suggesting that two dominant genes, one an inhibitor, were controlling the trait. Breeding and selecting for aroma and intermediate gelatinization temperature could be accomplished relatively easily because the traits are simply inherited. The genetic variability for yield and yield related traits was wide and significant (P=0.05) in the F2 populations of Malawi rice landraces and NERICA varieties crosses indicating that the populations would be valuable sources to develop varieties with improved yield. Panicle weight and the number of panicles per hill were positively correlated with, and had high direct effects on grain yield, therefore they could be used to indirectly select for high yield. Grain yield, the number of panicles per hill and plant height were predominantly controlled by additive gene action suggesting that bulk breeding methods would be adopted for these traits. The days to 50% flowering, panicle weight and 1000-grain weight were predominantly under the control of nonadditive gene action suggesting that hybrid development would be profitable for these traits. Faya Mpata, Faya Zidyana and NERICA 3 could be the best parents for improving yield and yield related traits because they had high general combining abilities for the traits. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010.

The African Rice Gall Midge (AfRGM), Orseolia oryzivora Harris and Gagné (Diptera: Cecidomyiidae), is an endemic rice pest found throughout Africa. The failure of most other control methods imposes the need to use crop resistance. This study was initiated: (1) to develop an accurate method for assessing damage caused by AfRGM; (2) to determine AfRGM resistance genes’ modes of action, the heritability estimates of their resistance to AfRGM and the behavioural pattern of progenies with resistance to AfRGM attack; (3) to reveal convergent evolution of same or similar resistance gene(s) in geographically distinct landraces, or divergent evolution of genotypes carrying the same gene, by analysing the genetic diversity among five AfRGM parental lines; (4) to build a core sample of progenies to be used as a reduced mapping population, largely reflecting the entire genome of the whole population, after an estimate of the heritability of 15 agro-morphological descriptors and; (5) determine Simple Sequence Repeat (SSR) markers flanking genes or quantitative trait loci (QTLs) linked to resistance to AfRGM. A method of accurately assessing damage caused by AfRGM was determined by comparing four methods of assessment including the International Rice Research Institute’s (IRRI) Standard Evaluation System (SES) for rice and three methods based on resistance index (RI) assessments differing in the computing of the percentage of tillers with galls on a resistant check variety. The RI-based assessment (RI-BA) methods consistently provided a better evaluation of AfRGM damage than the SES, regardless of the trial size. Within RI-BA methods, RI-BA2 was always more accurate than RI-BA1 and RI-BA3 when the plot was large. RI-BA2 and RI-BA3 were equally accurate when the plot size was small, and they provided better estimates than RI-BA1. When the plot was of medium size, RI-BA2 was more accurate than RI-BA3; RI-BA3 also surpassed RI-BA1. Overall, the best method of assessing AfRGM damage was RI-BA2, regardless of the plot size. Five rice populations including F1, F2 and F3 generations involving ITA306, a susceptible variety of Oryza sativa subsp. indica, and four varieties having different reactions against AfRGM were used to determine the genetic basis of resistance and estimate the heritability of resistance to AfRGM. All the F1s were susceptible, suggesting recessive gene inheritance. The F2 generations’ segregation pattern of 1R:15S in both ITA306-TOS14519 and ITA306-TOG7106 crosses as well as the segregation of 1R:8Seg:7S in ITA306-TOS7106 F3 families indicated that the AfRGM resistance expression being studied is governed by two genes. The deviation of the segregation patterns of crosses involving ITA306 and the tolerant parental lines from Mendelian segregation ratios suggests that the tolerance to AfRGM shown by BW348-1 and Cisadane is under complex mechanisms of control rather than under simple genetic control. The narrow-sense heritability estimates of resistance to AfRGM were low in populations involving tolerant varieties and were high in populations involving resistant varieties. They ranged from 0.086 in the ITA306-Cisadane population, to 0.4 in the ITA306-TOG7106 population. Conversely, the broad-sense heritability estimates ranged from 0.23 (ITA306-Cisadane) to 0.63 (ITA306-TOS14519). The behavioural patterns of progenies against AfRGM attack were evaluated for 532, 413 and 479 F2 progenies from ITA306-BW348-1, ITA306-Cisadane and ITA306-TOS14519 crosses, respectively, in addition to 90 BC1F2 progenies from the ITA306 and TOG7106 cross. One F3 generation of 649 families from a cross between ITA306 and TOS14519 was also tested. Four types of behavioural pattern categories were observed: (1) progenies were more resistant than the resistant check entry at 45 DAT and 70 DAT; (2) progenies were more resistant at 45 DAT and became susceptible at 70 DAT; (3) progenies were susceptible at both 45 DAT and 70 DAT; (4) progenies were susceptible at 45 DAT but reverted to resistant at 70 DAT. The first three categories were the most frequently observed and occurred in all cross combinations. The last category was observed only for a few progenies from the ITA306-TOS14519 F2 and F3 generations and, surprisingly, many from the ITA306 and BW348-1 cross. Heritability estimates were calculated for 15 major traits in an F3 population in order to predict the genetic gain associated with each trait, together with the resistance to AfRGM and to estimate the influence of the environment on phenotypic values. Broad-sense heritability (H2) estimates were high for the penultimate leaf length (PLL) - 0.99, penultimate leaf width (PLW) – 1.0, flag leaf length (FLL) - 0.99, flag leaf width (FLW) – 1.0, ligule length (LigL) - 0.99, tillering ability (Til) - 0.99, number of days to booting (DB) - 0.95, number of days to first heading (DFH) - 0.96, number of days to heading (DH) - 0.89, number of days to maturity (DM) - 0.98, culm length (CL) - 0.99, plant height (PH) - 0.99, panicle length (PanL) - 0.95, secondary branching (SB) - 0.95 and the thousand grains weight (TGW) - 0.71. Conversely, narrow-sense heritability estimates were very low (nearly 0) in PLL, FLL, Lig, DB, DFH, DM and SB or low (at most 0.267) in PLW, FLW, DH and PH, with a high value of 0.727 for TGW. Inheritance of the traits studied was therefore under non-additive gene effects rather than additive genetic effects and can therefore be improved using pedigree breeding schemes along with breeding for AfRGM resistance. Fine genetic evaluation of five AfRGM parental lines was studied in terms of polymorphisms using 303 SSR primers covering the rice genome. Of the 178 polymorphic primers identified, 60 were highly polymorphic and informative. The number of alleles amplified by these primers ranged from one to five for a total of 1,041 alleles. The polymorphism rate was globally high, ranging from 45.2% to 66.8%. The mean of the polymorphism information content (PIC) was 0.553. Factorial analysis, based on the allelic diversity, demarcated the parental lines into Oryza glaberrima Steud, Oryza sativa subsp. japonica and O. sativa subsp. indica groups, while a cluster analysis distinguished them into four groups: AfRGM resistant, susceptible, moderately resistant and tolerant. BW348-1 and Cisadane showed the least diversity, despite their distant geographical origins. TOS14519 and TOG7106 showed more divergence to ITA306 despite their common West African origin. This variability amongst the genotypes tested is the result of farmer-based selection for AfRGM resistance rather than direct breeding efforts through breeder intervention. A method of selecting individuals for a mapping population, based on a core sample, was developed in order to speed up the mapping procedure. A diversity study amongst F2 and F3 generations involving 15 quantitative and 26 qualitative agro-morphological characters was carried out and led to the dropping of seven non-discriminant descriptors. The diversity index (H) was calculated for each remaining character and the discriminant descriptors were selected based on a diversity index threshold value above 0.4. Four descriptors of H values less than 0.35 were therefore dropped. The sizing of the core collection of 64 individuals and the selection of these individuals were done using MSTRAT version 4.1 package in redundancy mode, a construction run of 100 times with an iteration number of 500. The core sample was similar to the whole population for clustering pattern, minimum and maximum quantitative values and diversity index, while mean values and coefficient of variation distinguished them. The core sample, which represents 10% of the whole population, also revealed the same phenotypic variation and the same genotypic segregation according to two SSR markers. It can therefore efficiently reflect the whole population as a mapping population. Finally, a study was undertaken to identify flanking markers to the gene/QTL involved in the resistance against AfRGM using bulked segregant analysis (BSA). A polymorphism study between ITA306 and TOS14519 displayed 145 polymorphic SSR markers, which were used to screen the bulks that originated from the two tails, and depicted only two SSRs as candidate markers linked to gall midge resistance. These markers included RM317 and RM17303 which displayed strong significance after an analysis of variance using an F test, meaning that they were segregating with the resistant alleles. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.

Genetic resources are important for the development of every country and for humanity. Collection, conservation and reasonable utilization of genetic resource is required mission. Understanding the importance of genetic resource, especially rice germplasm, since 2001, Center for conservation and development of crop genetic resources (CCD-CGR) of Hanoi University of Agriculture (Vietnam National University of Agriculture) has been collected, conserved and evaluated rice germplasm from different provinces of Vietnam for breeding programs. So far, 1090 accessions of local rice of Vietnam have been collected. Evaluation of agronomic properties and screening of some important genes using DNA molecular markers have revealed that Vietnamese rice germplasm has high level diversity and containing important genes for quality and resistance for disease and pests. These genetic resources are potential materials for national breeding programs. Based on the collected germplasm, 3 new glutinous rice varieties have been successfully created with high yield and good quality. In addition, the degradation of local rice varieties is also a matter of concern. So far, 4 specialty rice varieties Deo Dang, Ble chau, Pu de and Khau dao have been successfully restored for the north provinces of Vietnam. The main results of this study are germplasms for rice breeding programs and new improved varieties that bring economic benefits to farmers and the country. / Nguồn gene là tài nguyên sống còn của mỗi quốc gia và của toàn nhân loại. Vì vậy thu thập, bảo tồn, đánh giá và khai thác hợp lý nguồn tài nguyên này có ý nghĩa rất lớn. Nhận thức được tầm quan trọng của nguồn gen nhất là nguồn gen cây lúa, ngay từ đầu những năm 2000, Trung tâm bảo tồn và phát triển nguồn gene cây trồng thuộc Trường Đại học nông nghiệp, nay là Học Viện nông nghiệp Việt Nam đã tiến hành thu thập, lưu giữ, đánh giá và khai thác nguồn gene lúa. Kết quả đã thu thập, lưu giữ được 1090 mẫu giống lúa địa phương Việt Nam. Đánh giá đặc điểm nông sinh học và phát hiện một số gene quy định các tính trạng chất lượng và kháng sâu bệnh bằng chỉ thị phân tử DNA. Đây là nguồn gene quan trọng cho chọn tạo giống. Dựa vào nguồn gene thu thập được, cho đến nay, Trung tâm bảo tồn và phát triển nguồn gene cây trồng đã lai và chọn tạo được thành công 03 giống lúa nếp chất lượng cao. Ngoài ra, thoái hóa giống cũng là vấn đề đang được quan tâm. Cho đến nay 4 giống lúa đặc sản Đèo đàng, Ble châu, Pu đe và Khẩu dao đã được phục tráng và đưa vào sản xuất. Kết quả của những nghiên cứu này là ngân hàng các giống lúa làm nguồn gene để chọn tạo giống mới đem lại lợi ích kinh tế cho người nông dân và đất nước.

Rice production in Sub-Sahara Africa is hampered by drought stress, low farmer adoption of improved varieties, un-adapted germplasm, problems of crossability between species and problems of efficient emasculation. This study was initiated to: (1) determine farmer preferences for rice varieties and production practices, (2) identify drought tolerant parental lines for use in interspecific crosses, (3) determine crossability between different rice species, (4) identify drought tolerant interspecific segregants from crosses, and (5) study the efficacy of ethrel and gibberrilic acid (GA3) as chemical hybridising agents. Participatory rural appraisal (PRA) was conducted in Sikasso region in the month of September 2005 to determine farmer preferences for varieties and production constraints. A total of 125 rice farmers from 10 villages participated. This study found that farmer preferences for rice traits did not coincide with the breeders' objectives and trait preferences varied across ecologies. In upland and lowland rice ecologies, the most preferred characteristic was short duration. In the lowland tall plants was most preferred and short duration trait ranked second. Long duration ranked as the second most preferred trait after yield in the irrigated rice ecology. The estimated grain yield reduction was 60% due to drought stress from all ecologies. Sixteen genotypes including seven Oryza glaberrima Steud, six interspecific (0. saliva x 0. glaberrima) inbred genotypes and two improved 0. saliva L. subsp Gaponica) genotypes, with OS 6, as drought tolerant check were screened for drought tolerance at the vegetative stage during the dry seasons of 2004 and 2005 at Samanko research station, in Mali. Most of the genotypes could be regarded as exhibiting drought tolerance and avoidance mechanisms for most of the morpho-physiological characters under study. High selection index was observed for WAB 450-I-B-P-103-HB in the two season experiments. Drought stress tolerance (little leaf drying) was significantly correlated with leaf rolling, leaf area index, and plant height. Fast drought recovery was significantly correlated with drought tolerance, tiller number and leaf area index. Effects of genotypes, environment and their interactions were significant for tiller number, root dry weight and relative leaf water content. The most stable genotype was RAM 3 for tiller number and relative leaf water content. Thirteen genotypes were selected on the basis of these traits for rice hybridisation. A factorial arrangement involving three levels of gametocide concentrations and five application stages of the female rice parent was undertaken for each gametocide ethrel and GA3 for two seasons. Per cent empty spikelets and male sterility increased with concentration of ethrel. Male sterility induction of 41.5% and 42.8% at 2000 ppm was achieved in 2004 and 2005, respectively, while at 4000 ppm male sterility induction was 40.5 % and 46.1% in 2004 and 2005, respectively. The best application stage of ethrel that induced highest male sterility was at P4 (panicle primordium differentiation + spikelet primordium differentiation) of 46.6% in 2004 and 49.2% at PI (panicle primordium differentiation) in 2005. There was no measurement on GA3 for sterility due to lodging. Total male sterility was not achieved therefore, these gametocides could not be recommended for use as hybridising agents. Crossability was studied in four groups: group A (0. glaberrima x 0. saliva), group B (0. glaberrima x Interspecific), group C (Interspecific x 0. saliva) and group D (Interspecifics x Interspecific). High percent seed set was obtained in group D of 19.08% and group A had 9.29%, in group B the seed set was 11.26% and group Chad 6.62 %. The three best combiners as female parents based on percentage seed set were CG 14 (0.glaberrima), WAB 450-IBP-I05-HB and WAB450-I-B-P-I03-HB (interspecifics), and for male parents were NERICA 3, NERICA 2 (interspecifics) and WAB 375-B-9-H3-2 (0. sativa). Genetic components of variance and heritability estimates were studied in F3 and F4 generation progenies from North Carolina II design mating scheme. General combining ability (GCA), manly due to female and specific combining ability (SCA) were significant for tiller number, plant height and specific leaf dry weight indicating that additive and non-additive genetic effects controlled these traits. Heritability estimates for drought tolerance and leaf rolling were highly significant for all the populations examined, ranging from 0.32 to 0.72 and 0.22 to 0.56, respectively. Drought tolerance expressed as little leaf drying was significantly associated with less leaf rolling, larger leaf area index, and taller plants. Some genotypes and progenies such as WBK 39-B-B-B, WBK 30-B-B and WAB 450-I-B-P-I03-HB were identified as being drought tolerant with the ability to recover quickly from drought stress. There was a strong desire for tall plants and short duration rice in upland and lowland ecologies, while high yield was preferred in irrigated ecology. Therefore, the best breeding strategy would be ecosystem breeding targeting each of the ecologies. Screening for secondary traits that have been identified to be significantly associated with rice grain yield could be used for direct selection for grain yield under drought stressed conditions. Progenies identified, as drought tolerant would be considered for use as source germplasm in breeding that target Sikasso region and any other similar ecologies. This study therefore suggested that participatory research approaches that involve all stakeholders in rice production would be valuable in identifying and generating drought tolerant and adoptable rice cultivars in the tropics of Africa with considerable impact on food security. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2006.

Grain yield of rice can be enhanced by breeding for drought tolerance and optimum shattering. New generations of rice, the interspecific fixed lines known to carry more drought tolerance traits, are a potential source for improvement of the Ugandan landraces but they frequently carry genes for grain shattering. Information gathered through surveys to understand rice production constraints and farmers’ preferred rice traits are limited and they are generally unranked. The objectives of this study were seven-fold. They were to 1) determine farmers’ perceptions on the key production constraints and preferences for rice in Uganda, 2) develop and appraise cheap and efficient rice breeding equipment, 3) determine anthesis and the grain shattering pattern of rice, 4) characterize for drought tolerance and grain-shattering ability in rice populations in Uganda, 5) investigate crossability between O. sativa and the new interspecific fixed lines, and 6 and 7) determine the inheritance and gene action controlling drought tolerance and grain shattering traits. The experiments were conducted at Namulonge, Uganda, from 2006 to 2009. Data on farmer’s perceptions of the key production constraints and preferences for rice in Uganda were obtained through participatory rural appraisal (PRA) methods and a formal household survey of 380 farmers from three regions in Uganda during March 2007 to June 2008. The results showed that the variety NERICA 4 was the most preferred by farmers. Rice yellow mottle virus disease, rice blast and African rice gall midge were major constraints under lowland conditions, while drought was the major constraint under upland conditions. The preferred traits in traditional varieties included aroma characteristics, grain size and the texture of cooked grains. Cultivars that combine high yield potential, early maturity, drought tolerance, aroma characteristics and special market attributes should be included in the breeding objectives. A new anther suction device that uses an ordinary household vacuum cleaner was fabricated. Its overall units include a pipette tip, silicone tubing, hose tubes, a metallic stand, a rubber stopper and a household vacuum cleaner of 1600 w capacity. It is efficient, cheaper, less bulky and has lower replacement costs than the commercial one. In addition, a hand-held single grain tester, which is efficient, cheaper and more suitable for field studies than the laboratory tester, was developed and appraised. Studies to determine the grain-shattering pattern in rice were conducted by making assessments at 10, 20 and 30 days after anthesis. The results revealed that the highest level of discrimination among the varieties was between 10 days and 20 days after anthesis. Among the genotypes tested, NERICA rice attained anthesis earlier than CT rice and O. sativa attained anthesis later than both rice groups. Appropriate methods of planting the parental lines were proposed for pollination to be synchronised. Interspecific rice and O. sativa were characterized in the field for drought tolerance and grain-shattering ability. There was high variability wihin species in grain shattering and drought tolerance traits, suggesting that selection could be effective. The distribution of grain shattering scores was not normal, suggesting that some selection had taken place for the trait, unlike the drought tolerance traits and leaf roll scores where normal distributions were observed. Results of the crossability test between O. sativa and interspecific fixed lines revealed that some genotypes had high crossability when used as males, or as females, or as both females and males. The best male genotype combiners were CT 16334(2)-CA-2-M, WAB 365-B-1H1-HB and IRAT 257, while the best females combiners were CT 16334(2)-CA-11-M, CT 16317-CA-4-M and IRAT 325. In addition, additive effects were more important that non-additive effects for pollen viability and seed set in the crosses. Genotypes with acceptable crossability and varying levels of drought tolerance and grainshattering ability were selected for further studies. The selected genotypes were crossed in a North Carolina II mating scheme, and as pairs of crosses, and used to understand the genetic mechanisms of drought tolerance at the reproductive and vegetative stages. Evaluation of the populations revealed that additive effects for filled grains were more important under drought stress and non-drought stress conditions than the non-additive effects. There were high heritability estimates for leaf roll under drought stress, implying that additive effects were more important. There was a higher contribution of additive effects for grain-shattering ability than nonadditive effects in the populations. Allelic tests for the shattering trait revealed that a single gene was in 46% of the crosses; two genes in another 46% of the crosses had duplicate dominant effects as well as complimentary dominant/recessive effects; and there were three genes in four percent of the crosses. Segregation ratios of 3:1 and 1:3 were also found in two crosses. This could be due to a reversal of the function of the genes. Another surprising finding was that the segregation ratio of 3:1 was found in a cross with loose grain attachment to the pedicel in an allelism test. This segregation was probably due to unfixed loci in some of the interspecific lines. This study identified rice breeding priorities for Uganda, prepared breeding tools and provided relevant information for generating lines that have improved drought tolerance and optimum grain-shattering ability by determining the modes of gene action for these two traits. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010.

Rice (Oryza sativa L.) is the principal crop of North Eastern Tanzania but production is threatened by salt affected soils, drought and the use of un-adapted cultivars, among other constraints. Little research and hardly any breeding have been done on the aspects of salt tolerance of the crop in sub Saharan Africa, leading to low yields and low production in rice irrigation schemes under arid and semi arid conditions. A project was therefore implemented in North Eastern Tanzania during 2007-2010 seasons to investigate the possible breeding contributions to enhance productivity and production of the crop in salt affected areas. The objective of this study was to: a) determine farmers’ perceptions on both salt problems and their effects on rice crop productivity as well as establishing farmers’ needs and preferences for rice varieties in the targeted irrigated environment; b) determine the extent of salt problem in both soil and irrigation water in the available rice irrigation schemes in the North-eastern Tanzania; c) identify the major physiological mechanisms associated with salt tolerance in farmer-preferred native varieties and landraces; and d) determine the mode of inheritance of salt tolerance in rice. Participatory rural appraisal was conducted in Mkomazi and Mombo villages in Tanga region with the aim of understanding characteristics of rice–based farm economy, farmers’ perception of agriculture constraints and variety preferences in salt affected areas of North-eastern Tanzania. This was followed by a preliminary study to understand soil characteristics in relation to salt problems and its extent in selected nine rice irrigation schemes. Studies was established under controlled conditions to assess the salt tolerance of some rice farmers preferred rice cultivar and evaluate the putative traits in the rice materials that contribute to the performance of a genotype under saline and saline-sodic condition. Thereafter, genetic mechanism governing various morpho-physiological parameters in selected Tanzania local farmers’ preferred varieties and salt tolerant donors under saline and sodic soil conditions of North Eastern Tanzania were determined. A participatory rural appraisal (PRA) established that rice was a major staple food and cash crop and rice farming was a major economic activity in the area. However, soil degradation through increased salt affected soils was identified as the major factor responsible for irrigated rice yield decline. Major varieties grown are salt sensitive, and salt tolerant varieties were not available. The study also revealed that most farmers’ preferred traits of rice cultivars were high yield potential, aroma, early maturing, medium plant stature, tolerance to salt and drought. Improvement of these characters in new salt tolerant varieties would increase food production in fields with low or zero productivity and the well-being of the poor farmers. A soil characterisation study indicated the magnitude of the problem, whereby, seven out of nine studied irrigation schemes were affected and sodic and saline-sodic conditions were the dominant types of soils. Poor irrigation canals and management of irrigation water were the driving factors that contributed to salts accumulation causing a decline in productivity. Experiments were established under controlled environments to evaluate the tolerance of 10 and 11 rice genotypes under saline and saline-sodic stresses, respectively. Significant variation between genotype and significant interactions between genotype and salt treatment (P<0.001) were observed for all characters studied. Genotype Pokkalli, IR 67076-2B-21-2 and IR 56 showed superior performance under saline, whereas CSR 27, Nerica 2 and IR 56 had superior performance under saline-sodic. The study therefore established that, all the local farmer preferred cultivars except IR 56 performed poorly under both salt stress environments. High seedling vigour, less leaf injury, less Na+ and high K+ accumulation in leaves, low Na+/K+ ratio of ion uptake, high spikelet fertility, increased grains per panicle and 1000 grain weight were considered as the desirable characteristics therefore can be used in developing lines for salt tolerance for production under saline and saline - sodic conditions. Gene action and combining ability studies for nine morpho-physiological traits were studied under normal, saline and sodic soil environments. The rice populations were generated through 7 x 7 full diallel crosses and advanced to F2. The parents comprised two donors for saline tolerance, one donor for sodic tolerance and four salt sensitive farmers preferred varieties. Both additive and non-additive gene effects were important in the inheritance of the characters studied in all soil environments. However, additive effects were more important for the number of tillers, shoot Na+, Na+/K+ ratio and plant height. Both additive and non-additive gene effects were important for spikelet fertility, days to 50% flowering, number of grains per panicle, 1000 grain weight, and grain yield; however the magnitude of additive gene effect was higher than non additive effects. Amongst the parental lines, the best general combiners for yield along with other traits were TXD 306 and IR 67076-2B-21-2 under normal non-saline/sodic condition; IR 56, Pokalli and TXD 306 under saline condition and CSR 27 and TXD 306 under sodic conditions. The overall results from this study indicated the possibility of improving both yield and salt tolerance from this set of germplasm; therefore contributing to increasing rice yields in the marginal salt affected environments. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010.

Rice is an important crop ranking third after maize and wheat in Kenya. Its demand is growing at 12% per annum, while production has stagnated for quite a number of years. This situation has lead to consumption outstripping production by about 84%. There is therefore an urgent need to step up domestic production. To understand farmers’ preferences, the first survey on rice production was carried out. To supplement on this survey information, focus group discussions and key informants were incorporated to further shed more information. The farmers demonstrated their preferences for varieties that were high yielding, hybrid rice and with high nutrient use efficiency and these constituted 53.7% of their wishes. Among the crops grown by the selected farmers, rice was the most important followed by maize, however, the hectarage of maize was higher followed by rice. The farmers also identified labour costs as a factor limiting production especially for irrigated rice and thus they preferred upland rice due to its ease of production. Farmers identified land preparation, inputs, planting, weeding and harvesting as the most expensive activities. The existing varieties were viewed as being highly dependent on inputs which they could not afford. The main fertilizers used were Diammonium Phosphate (DAP), Sulphate of Ammonia (SA), Calcium Ammonium Nitrate (CAN) and NPK (23:23:0), the amounts used were low even though the farmers were aware that soil fertility was low. No studies or attempts had been carried out to determine performance of rice genotypes and their heritability parameters for adaptation to low soil nitrogen (N) and phosphorous (P) conditions identified by the farmers as a major constraint in Kenya. Since the existing genetic base was narrow, accessions were acquired to broaden the variability of the local cultivars. However, their adaptation to local conditions was important for them to be useful. Evaluation of 390 accessions showed that genotypes and soil environments were highly significant for all the ten traits studied. The degree of genetic determination (H(2)) ranged from 8.0% for 1000 grain weight to 27% for top biomass. The phenotypic coefficient of variation of genotypes ranged from 12% for days to maturity to 149% for top biomass, while, that of days to maturity ranged from 14% to 160% for top biomass. The genetic advance (GA) had values ranging from, 0.2 for phosphorous tolerance to 1081 for grain yield, while the genetic advance expressed as percent of the mean was 6% for days to maturity and 88% for top biomass. The mean values for the ten characters studied had wide variability under the four soil environments with days to maturity ranging from 188 for genotype ARCCU1Fa1-L4P3-HB under both N and P application (N+P+) to 177 for genotype CT16333(1)-CA-1-M under none N and P application (N-P-) condition. The highest yielding genotype was CT16328-CA-18-M under none N and P application with 5916 kg ha(-1). The germplasm revealed usable variability under low soil N and P adaptation and thus warrant rice improvement for traits of interest to farmers. In order to establish the genetic factors controlling upland rice adaptation to contrasting soil N and P a study was conducted to determine genotypes with better performance under the prevailing farmers’ production environments. The GCA and SCA mean squares were significant and their interactions with environment were highly significant. The GCA:SCA ratios were mostly less than 1.0 for the majority of the traits under most of the soil N and P environments, indicating preponderance of nonadditive genetic effects. The maternal and nonmaternal mean squares were significantly different from zero (P<0.05) for most of the ten traits under study, indicating influence of cytoplasm effects and cytoplasm by nuclear gene interactions, respectively. The GCA effects for the parents were significant under different experimental environments but they had both positive and negative signs indicating different directions of influencing the trait of interest. The genotypes had both specific and broad adaptation as exhibited by their diverse rankings under different environments. The relationship between leaf and grain nitrogen (N) and phosphorous (P) with actual tolerance to low and high soil N and P conditions indicated significant genotypes, environments and genotypes by environment interactions. The analysis of genetic components gave highly significant GCA and SCA mean squares for the days to heading, anthesis and maturity, phosphorous and nitrogen tolerance, top biomass, plant height, number of panicles, 1000 seed weight and grain yield under the four soil experimental environments. The general combining ability (GCA) effects for parents were significant for both F(2) and F(3) segregants for the above ten traits and under the experimental conditions. The leaf and seed N and P contents gave significant genotype mean squares values for the three mega-environments. The GCA and SCA mean squares were significant for leaf and seed N and P for the three locations. The same case was observed for GCA effects for the parents, with all the nine parents showing significant values for leaf N and P for the three locations. The GCA:SCA mean square ratios were generally larger than 1.0 values for leaf N and grain P for the three locations. This clearly manifested the predominant role of additive gene action over the dominance effects and that improvement for tolerance to low soil N and P condition was practical. The fragrance in rice is an important quality traits and an experiment was conducted to establish the association of organoleptic test and the variations in SSR marker (RM223) among the parents. Plant leaves of the parental genotypes were sampled for DNA analysis using SSR markers RM223 and RM284. The RM223 was polymorphic while, RM284 gave monomorphic results. Four alleles were detected as follows: 146, 155, 161, and 163. The GCA:SCA ratio was 1.48 indicating that the fixable additive effects were greater than the nonadditive effects in inheritance of fragrance. Test for independence using Chi-square indicated that there was no association between organoleptic and variations in SSR markers. The performance of the aromatic lines was generally lower than that of non-aromatic lines for the agronomic traits. There was negative relationship between fragrant score and other agronomic traits such as grain yield across the three soil N and P regimes. The NERICA1 was found to be a good donor for aroma based on sensory testing and can be exploited in a breeding programme. Analysis on genetic components governing grain yield was investigated using Hayman’s analysis to generate various components of variation and to elucidate their potential, utilization, and provide a thorough understanding of their role in grain yield development and improvement. The additive gene action was significant for all cases of soil N and P environments and the two mega-environments. They were also far above the dominant gene effects, indicating the need to use mass selection in the early generations of segregating populations. The narrow sense heritability (h2(ns)) for upland rice grain yield was 21.52% and 4.22% under soil P and N conditions, respectively. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2010.

The main goals of this study were to ascertain farmers' preferred traits in rice landraces and their perception of Rice yellow mottle virus, to collect rice landraces across Burkina Faso, investigate their genetic diversity, and to exploit this diversity in a search for varieties resistant and tolerant to RYMV, for their utilisation in rice breeding. Farmers' preferred traits, approaches to crop management, and disease perceptions were assessed using a Participatory Research Appraisal (PRA) approach. In the main rice growing regions of Burkina Faso, 330 rice landraces were collected. The agro-morphological diversity of the germplasms was evaluated in the field with 20 quantitative and 30 qualitative agro-morphological parameters. Thereafter, 22 Simple Sequence Repeat molecular markers were used to assess the genetic diversity and the population structure of the collection. Finally, the rice landraces were screened against four RYMV isolates to assess the susceptibility, tolerance and resistance of the landraces in the collection using visual assessment and Enzyme Linked Immunosorbent Assay. The PRA identified sweet taste, grain expansion when cooking, easy cooking and yield as paramount selection criteria in rural rice farming communities in Burkina Faso. Drought and disease resistance are characters that farmers wish to have in their varieties. The PRA also highlighted that farmers are conscious of RYMV disease in their fields. However, they are unaware about the epidemiology of the disease. An agro-morphological study of the phenotypic diversity of the collection confirmed the presence of the two cultivated rice species: O. glaberrima and O. sativa. There were more O. sativa accessions than O. glaberrima landraces. There were 48 O. glaberrima and 282 O. sativa accessions in the collection. Both species were divided into four clusters, reflecting the richness of the collection. The underlying genetic diversity of the collection was confirmed by the use of 22 Simple Sequence Repeat molecular markers. The neutral markers confirmed the existence of two substructures, namely O. glaberrima and O. sativa, and the presence of admixture varieties. However, a core collection of 52 individuals was developed. This included 13 O. glaberrima and 39 O. sativa accessions. It reflects the genetic diversity of the sub-clusters present in each species. This core collection contains 89% of the allelic richness of the collection. Its small size will facilitate the maintenance and active use of diversity of germplasm in the core collection. The entire collection was utilised to search for varieties resistant and tolerant to RYMV disease. The screening of the collection with different RYMV isolates exposed the susceptibility of most of the accessions in the collection. Most of the O. sativa indica accessions were highly susceptible. However, ten O. glaberrima accessions displayed a delay of symptom expression, and moderate resistance. However, their resistance was overcome later by a particularly virulent RYMV isolate BF1. Remarkably, a single moderately resistant cultivar, BM24, showed that partial resistance and tolerance to RYMV can be found in an O. sativa variety. Serological evaluation of this local variety in comparison with the partially resistant variety, Azucena, showed that BM24 and Azucena expressed similar resistance patterns. A genetic profile of both varieties showed that both had an identical allele status at RM101, which is a marker bracketed in the same zone as the QTL12. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2011.