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Studies of drought tolerance in interspecific progenies of Oryza glaberrima (Steud) and O. Sativa (L) and an appraisal of the use of male gametocides in rice hybridisation.Efisue, Andrew A. January 2006 (has links)
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.
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Genetic studies on drought tolerance and grain shattering in rice.Lamo, Jimmy. January 2010 (has links)
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.
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Breeding investigations for salt tolerance in rice incorporating characterisation of salt affected soils and farmers perceptions and preferences for tolerant cultivars in north-eastern Tanzania.Kashenge-Killenga, Sophia. January 2010 (has links)
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.
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Genetic studies of quantitative and quality traits in rice under low and high soil nitrogen and phosphorous conditions, and a survey of farmer preferences for varieties.Munji, Kimani John. January 2010 (has links)
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.
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A study of the diversity of Burkina Faso rice landraces and identification of source of resistance to rice yellow mottle virus (RYMV)Kam, Honore. January 2011 (has links)
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.
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Genetic diversity of Oryza species in Niger ; screening and breeding for resistance to rice yellow mottle virus (RYMV)Sow, Mounirou El-Hassimi. January 2012 (has links)
Rice is a staple food in many West African countries, including Niger. However, both regional and national rice production have failed to meet demand due to several constraints, among which is the Rice yellow mottle virus (RYMV). Moreover, attempted intensification of rice cultivation and the introduction of modern cultivars are encouraging farmers towards abandoning local landraces for high yielding, but often susceptible varieties. The study was primarily oriented towards rice pre-breeding, and identifying priorities for rice breeding in Niger in relation to farmers' preferences and their environment. A secondary aim was the development and evaluation (for release at the regional level) of new breeding lines with resistance to RYMV. This study aimed to: 1) Establish farmers' perception of rice varieties as well as the main constraints on rice production in Niger and particularly those posed by RYMV; 2) Create a collection of rice species from Niger for ex- situ conservation, and to determine the phenotypic variability within this collection; 3) Determine the genetic diversity and population structure of the collection; 4) Screen the collection for resistance to RYMV, so that new sources of resistance could be detected; 5) Improve five elite varieties from West Africa for resistance to RYMV using marker-assisted selection (MAS). The germplasm collection and PRA of this study were conducted in 2008 and 2009 in Niger, while the field and the laboratory researches were conducted in 2008 and 2009 at the Africa Rice Center (AfricaRice) in Benin. For the PRA, data was obtained from a semi-structured group discussion carried out in 14 villages, individual questioning of 153 farmers and visits to farmers' field and storage facilities. The local farmers' union was the only formal seed dissemination system. Seed exchanges between farmers and the use of seeds from previous harvests were important. The RYMV and the bacterial leaf blight (BLB) were cited as the prevalent biotic stresses in the irrigated agrosystem, where the varieties IR1529-680-3 and Waihidjo were found to be the most popular. Flood, birds and hippopotamus were the most damaging agents in the lowland cropping system, and the landrace Degaulle/ D5237 was the preferred variety. Apart from the yield, farmers preferred varieties with good grain quality (milling quality and good taste), high market value, stress tolerance (drought, flood, disease, birds, rodents), and those recommended by the local farmers' association. These findings should be included in breeding goals, seed production and dissemination systems. During collection, a total of 270 rice accessions were assembled, comprising the two cultivated rice species Oryza sativa L. and O. glaberrima Steud. and its two wild relatives Oryza barthii A. Chev. and O. longistaminata Chev. et Roehr. The region of the Niger River and its tributary (the Dallol Maouri) provided the majority (80.7%) of the accessions. Apart from a few wild O. barthii accessions, the accessions found around Lake Chad and the Komadougou river (South-East) were also collected in the Niger River area. Farmers' naming and ecological classification of rice varieties was generally consistent. Three major phenotypic groups were found during the field trials, and the overall phenotypic variability of the collection (as measured by the Shannon-Weaver Diversity Index) was relatively high. There was no significant difference in diversity between the main eco-geographical zones of collection, as well as between the identified phenotypic groups, suggesting a high level of germplasm exchange between the regions in Niger.
From the collection, 264 accessions were genotyped from the collection using 18 well distributed SSR markers and two main genetic compartments were detected, comprising O. sativa subsp. indica varieties and O. glaberrima and its wild relative O. barthii and O. longistaminata. The O. sativa group in Niger was divided into irrigated and floating rice, bound by lowland rice. The wild progenitor O. barthii was widespread but without any clear genetic differentiation from O. glaberrima, probably due to the presence of admixtures within the collected samples of O. barthii. Allelic diversity was relatively high, despite the geographical distance from the centre of domestication of African rice, and the points of entry of Asian rice to Africa. The findings reflect the underuse of Niger's rice landraces genetic potential for rice breeding, given that all the "improved" varieties released during the last 25 years in Niger were clustered together on the dendrogram. The response of a set of the rice collected from Niger and some accessions from Mali to inoculation by RYMV was evaluated using five different virus isolates from Niger (3), Benin (1) and Burkina Faso (1). All rice varieties were susceptible to the disease. However, depending on the virus strain, a few O. glaberrima accessions displayed partial resistance, similar to the highly resistant TOG5681. Allelic research based on primers derived from the RYMV1 gene revealed one accession with allele rymv1-3, and two accessions with allele rymv1-4, and one accession with a different resistance gene. The implications of the finding were discussed and a strategy proposed for breeding varieties with a comprehensive resistance to RYMV.
After three generations of backcrossing, the major resistance gene of the variety Gigante was successfully introgressed into five elite rice varieties of West Africa by Marker-Assisted Backcross (MABC). The newly developed BC3F3 progenies were screened for resistance to RYMV in farmers' fields in Guinea and Mali and also under controlled conditions in a screenhouse in Benin. As shown by low virus content and level of disease incidence, low tiller number and plant height reduction, the transferred gene was fully functional in the new genetic background. Moreover, some lines also displayed a high level of resistance to rice blast (Pyricularia oryzae) and stem borer infestation in Guinea. Four of those lines are in the second year of multi-location trial in seven West African countries. Therefore, effective deployment of the newly developed varieties, coupled with good cultural practices, should reduce the damaging effects of RYMV in lowland and irrigated rice cropping systems and thereby increase the income of small scale farmers from rice cultivation. / Thesis (Ph.D.)-University of KwaZulu-Natal, Pietermaritzburg, 2012.
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