There is an increasing need to improve crop water-use efficiency (WUE) (ratio of whole-plant biomass to cumulative transpiration) due to decreased water availability and increased food and energy demands throughout the world. The objective of the study was to estimate the genetic variation and genetic basis for transpiration efficiency A:E (CO2 assimilation rate (A) divided by transpiration rate (E)) trait and its relationship to WUE related to pre-flower drought tolerance in recombinant inbred lines (RILs) of sorghum and associated QTLs. A greenhouse study was conducted at Bushland, TX, 2008, using 71 RILs derived from cross of Tx430 x Tx7078. A randomized complete block experimental design was used, with both genotype and water regime (40 and 80 percent water regime) as experimental factors, and four replications. Genotype had a significant effect on A, E and A:E under both the environments. Among the RILs, entry means for A:E ranged from 1.58 to 3.07 mmol CO2 mol^-1 H2O and 1.18 to 4.36 mmol CO2 mol^-1 H2O under 80 percent and 40 percent water regime, respectively. Heritability estimates based on individual environments for A:E , A and E were 0.77, 0.45 and 0.37 under 80 percent water regime and 0.90, 0.33 and 0.71 under 40 percent water regime, respectively. A genetic map was constructed by digital genotyping method using Illumina GAII sequencer with 261 informative indel/ single-nucleotide polymorphism (SNP's) markers distributed over 10 linkage groups. Three significant QTLs associated with transpiration efficiency were identified; two on SBI-09 and one on SBI-10 with one logarithmic of odds (LOD) interval length ranging from 5.3 to 5.7 cM and accounting for 17 percent - 21 percent of the phenotypic variation. In field and greenhouse evaluation of agronomic of traits at College Station and Halfway, TX, 91 QTL that control variation in six major agronomic traits such as plant height, flowering, biomass, leaf area, leaf greenness and stomatal density were identified. Co-localization of transpiration efficiency QTLs with agronomic traits such as leaf area, biomass, leaf width and stomatal density indicated that these agronomically important QTLs can be used for further improving the sorghum performance through marker assisted selection (MAS) under pre-flowering drought stress conditions.

Sorghum downy mildew (SDM) of maize is caused by the oomycete Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw. The disease can cause devastating yield losses in maize (Zea mays L.). Quantitative trait loci (QTLs) mediating resistance to SDM were mapped using both restriction fragment length polymorphisms (RFLPs), and simple sequence repeats (SSRs) in 220 F2 individual maize progeny derived from a cross between two extremes; highly susceptible inbred parent SC-TEP5-19-1-3-1-4-1-1 (white) and highly resistant inbred P345C4S2B46-2-2-1-2-B-B-B (yellow). The phenotypic expression was assessed on F2:3 families in a wide range of environments under natural field infection and in a controlled greenhouse screening method. Heritability estimates of disease reaction ranged from 93.3% in Thailand sit 1 to 48% in Thailand sit 2. One hundred and thirty three polymorphic markers were assigned to the ten chromosomes of maize with LOD scores exceeding 4.9 covering about 1265 cM with an average interval length between markers of 9.5 cM. About 90% of the genome was located within a 10 cM distance to the nearest marker. Three putative QTLs were detected in association with resistance to SDM in different environments using composite interval mapping. Despite environmental and symptom differences, one QTL on chromosome 2 bin 9 had a major effect in all trials and explained up to 70% of the phenotypic variation in Thailand where the highest disease pressure was experienced. Two other QTLs on chromosome 3 bin 5 and chromosome 9 bin 2 had a minor effect, each explaining no more than 4% of the phenotypic variation. These results revealed one major gene and two minor genes that control sorghum downy mildew resistance. These markers should be very useful in breeding programs in facilitating the introgression of the resistance genes into commercial varieties. Marker-assisted selection for these loci should be useful in incorporating SDM resistance genes in maize across environments, even in the absence of the pathogen.

Dry beans (Phaseolus vulgaris L.) contain high levels of folates. These compounds are essential vitamins and folate deficiencies may lead to a number of health problems. The objectives of this study were to examine the mode of inheritance of folate content and identify quantitative trait loci (QTL) associated with folate content in dry beans. Inheritance of folate content was studied in the F1 hybrids of one-way diallel crosses among Othello, AC Elk, Redhawk and Taylor, and an F2 population of the cross between Redhawk and Othello. Total folate content and 5 methyltetrahydrofolate (5MTHF) were measured twice within a one hour interval. Significant variation in folate content was observed among the parental genotypes, their F1 hybrids, and the F2 individuals of a cross between Redhawk and Othello, ranging from 147 to 345 µg/100g. Reductions in the 5MTHF content and total folate content values in the second measurement from samples were highly variable for all four parental lines ranging from 5 to 30% and 7 to 33%, respectively. A single marker QTL analysis identified at least three QTL for folate content in the F2 population. For the majority of identified QTL, dominance effects appeared to be the major genetic effect.

Recently designated as a bioenergy crop, Sorghum is rather unique as it can produce large quantities of cellulose or sugar which can be used to produce advanced biofuels or compounds. Sweet sorghum contains high levels of sugars and biomass sorghums consist primarily of ligno-cellulosic biomass. Improvement of both sorghum types is essential for maximizing production and conversion efficiency. Photoperiod sensitive sorghum is thought to maximize biomass production yet maturity influence on biomass production and composition is not fully understood. Utilizing sorghum for sugar production has increased efforts to develop sweet sorghums with sugar yields similar to sugarcane. Hybridization of these species has been investigated with, until recently, little success. Testing newly developed intergeneric hybrids and improvement of parents used in their creation will determine their feasibility and improve hybrid performance. Objectives of this research are multifaceted. First, analyze photoperiod sensitive sorghum in varying day length environments to determine maturity effects on plant phenotype, composition, and QTL detection. Second, analyze intergeneric sorghum × sugarcane hybrids to determine agronomic performance in relation to sugarcane. Lastly, introgress the iap allele into sweet sorghum females for use in intergeneric hybrid creation. Photoperiod sensitive sorghum RILs were evaluated in College Station and Weslaco, Texas and Puerto Rico which caused differential expression of plant maturity. Genetic control of trait expression was high for each location. Results indicate gradual induction of plant maturity increases detection of phenotypic QTL and detection of compositional QTL increases when maturity effects on plant phenotype are reduced. Intergeneric sorghum × sugarcane F_1 hybrids were compared to sugarcane in Weslaco, Texas in 2011. Each hybrid expressed agronomic traits similar or better than that of the sugarcane variety. High levels of repeatability and genetic influence on trait expression were observed. Overall performance of the sugarcane variety was better than any individual hybrid tested. Introgression of iap into sweet sorghum was successful and generated seventeen new sweet sorghum female genotypes possessing the allele. Only two genotypes exhibited higher brix readings and both were later maturing than Tx3361. Height and maturity of all developed genotypes varied and desirability of developed lines was similar to Tx3361.

Quantitative trait loci (QTL) analysis for Sclerotinia stem rot resistance was carried out in five doubled haploid (DH) populations of Brassica napus. Sclerotinia stem rot is caused by the necrotrophic fungus Sclerotinia sclerotiorum (Lib.) de Bary. Sclerotinia stem rot has worldwide occurrence and causes significant yield losses in many crop species. Several screening methods have been recommended in the literature to evaluate plant resistance to Sclerotinia stem rot. Four controlled environment based screening methods: 1) excised leaf assay, 2) cotyledon assay, 3) mycelial stem inoculation technique and 4) petiole inoculation technique compared for their ability to differentiate between plant susceptibility/resistance, their reliability and suitability for large scale screening using eight B. napus cultivars/lines of varying reaction to S. sclerotiorum. The petiole inoculation technique and the mycelium stem inoculation technique were identified as reliable methods in this study. Previously developed, five B. napus DH populations (H1, H2, H3, DH179 and DH180) segregating for resistance to Sclerotinia stem rot were used in this study. The petiole inoculation technique was used to evaluate resistance to Sclerotinia stem rot. Data on days to wilting was recorded for a two week period. Twelve plants per line were screened in each evaluation and each population was evaluated three times. Two to three day-old mycelial cultures of S. sclerotiorum isolate Canada 77 was used. QTL analyses were carried out using a LOD threshold value of 2.5 on each individual replicate and on the average of all the replicates. In the H1 population, the number of QTL detected ranged from four to six in each analysis. In the H2 population, there were three to six QTL in each analysis. There were two to six QTL in each analysis of the H3 population. In the DH179 population, the number of QTL detected ranged from three to five in each analysis. In DH180 population, the number of QTL identified varied from three to six in each analysis. A number of common QTL were found between the replicates of each population. Five common QTL were identified between these populations. The markers linked to these QTL are now available for marker assisted selection.

Glucosinolates are amino acid derived secondary metabolites found in the order Capparales. It is an important class of phytochemicals involved in plant-microbe, plant-insect, plant-animal and plant-human interactions. It is, therefore, important to understand genetic mechanism of glucosinolate biosynthesis in Brassica for efficient manipulation. In this study, QTL mapping of leaf and seed glucosinolates was performed in B. rapa using two RIL populations, SR-RILs and BU-RILs. QTL mapping was performed using SR-RILs developed from a cross of Chinese cabbage and turnip rapeseed and a genetic map in B.rapa. Genetic map was developed using a total 1,579 molecular markers including 9 markers specific to glucosinolate genes, GSL-ELONG, GSL-PRO, GSL-FMOOX1, and GSL-AOP/ALK. Several QTL for progoitrin, gluconapin, glucoalyssin, glucobrassicanapin, 2-methylpropyl and 4-hydoxyglucobrassicin glucosinolates were identified with phenotype variance between 6 and 54%. Interestingly, a major QTL for 5C aliphatic glucosinolates was co-localized with a candidate Br-GSL-ELONG locus on linkage group A3, displayed co-segregation with co-dominant SCAR marker BrMAM1-1. The Br-GSL-ELONG locus was identified to regulate 20 µmole/g seed 5C glucosinolate biosynthesis. BU-RILs derived from a cross of yellow sarson and USU9 was segregated for glucoerucin, gluconapin and progoitrin 4C aliphatic glucosinolates with 4-hydoxyglucobrassicin. Phenotyping was performed in controlled and field environments for seed glucosinolates and controlled environments for leaf glucosinolates. Genetic map was developed using SRAP markers and glucosinolate gene, GSL-ELONG and GSL-PRO specific 4 loci were integrated on map. Four and three QTL were identified for seed glucoerucin and gluconapin, respectively in both environments with phenotypic variance up to 49%. Additionally, genetic manipulation of glucosinolates was performed by backcross with MAS in B. rapa. Resynthesized B. napus line was backcrossed with B. rapa genotypes, RI16, BAR6 and USU9 for replacement or introgression of glucosinolate genes, GSL-ELONG- and GSL-PRO+. In RI16 genotype, 15 to 25 µmole/g seed 5C glucosinolates reduced in 15 BC3F2 lines those were positive with GSL-ELONG- marker and negative with the A-genome and gene specific marker BrMAM1-1. This suggests that the functional allele has replaced by non-functional from B. oleracea. GSL-PRO+ positive backcross lines in RI16 genotype displayed sinigrin 3C aliphatic glucosinolate in B. rapa. This suggests introgression of GSL-PRO+ in B. rapa.

A genetic linkage map of mustard (Brassica juncea) was developed using two double haploid populations produced from crosses between a low erucic cultivar “ZEM1” and two moderate erucic acid lines “Vniimk351” and “Vniimk405” with the use of SSR and SRAP markers. The linkage map of the ZEM1xVniimk351 population included 13 linkage groups with an overall length of 791 cM with an average marker interval of 5.7 cM. The linkage map of the ZEM1xVniimk405 population also contained 13 linkage groups with a distance of 623 cM and an average marker interval of 4.6 cM. Using the linkage maps for the two populations, QTLs were detected for seed oil, protein and fatty acids. QTL analysis for fatty acids indentified QTLs on LG1, 7 and 12 for the ZEM1xVniimk351 population and LG1, 3 and 4 for the ZEM1xVniimk405 population. Analysis for the seed oil and protein content in the ZEM1xVniimk351 population identified 2 QTLs on LG1 and LG4 and 1 QTL on LG1 respectively. The QTL analysis ZEM1xVniimk405 of oil and protein content identified 1 QTL for oil and protein on LG1. The variation of fatty acids was shown to be the result of monogenic inheritance of the FAE1 gene in both populations.

Cyanogenic glucosides (CGs) are bioactive plant secondary metabolites that can release toxic hydrocyanic acid when hydrolyzed. The accumulation of CGs in flax seed is a safety issue as a feed component and may contravene international trade restrictions. Here, we report the identification of major effect quantitative trait loci (QTL) for linustatin and neolinustatin, the two most abundant CGs in the mature flax seed. Current methods of CG analysis for screening and quality control are prohibitively expensive. Here, we also report on the development of a low cost, high throughput method of analysis using near infrared spectroscopy (NIRS) to estimate individual CGs and total hydrocyanic acid equivalent based on a regression of reference data obtained by gas chromatography. The genetic and physical mapping of the QTL and the NIRS calibration hold direct applications in the development of a flax breeding strategy for developing germplasm and cultivars with reduced CG content.

No description available.

Quantitative trait loci (QTL) analysis for Sclerotinia stem rot resistance was carried out in five doubled haploid (DH) populations of Brassica napus. Sclerotinia stem rot is caused by the necrotrophic fungus Sclerotinia sclerotiorum (Lib.) de Bary. Sclerotinia stem rot has worldwide occurrence and causes significant yield losses in many crop species. Several screening methods have been recommended in the literature to evaluate plant resistance to Sclerotinia stem rot. Four controlled environment based screening methods: 1) excised leaf assay, 2) cotyledon assay, 3) mycelial stem inoculation technique and 4) petiole inoculation technique compared for their ability to differentiate between plant susceptibility/resistance, their reliability and suitability for large scale screening using eight B. napus cultivars/lines of varying reaction to S. sclerotiorum. The petiole inoculation technique and the mycelium stem inoculation technique were identified as reliable methods in this study. Previously developed, five B. napus DH populations (H1, H2, H3, DH179 and DH180) segregating for resistance to Sclerotinia stem rot were used in this study. The petiole inoculation technique was used to evaluate resistance to Sclerotinia stem rot. Data on days to wilting was recorded for a two week period. Twelve plants per line were screened in each evaluation and each population was evaluated three times. Two to three day-old mycelial cultures of S. sclerotiorum isolate Canada 77 was used. QTL analyses were carried out using a LOD threshold value of 2.5 on each individual replicate and on the average of all the replicates. In the H1 population, the number of QTL detected ranged from four to six in each analysis. In the H2 population, there were three to six QTL in each analysis. There were two to six QTL in each analysis of the H3 population. In the DH179 population, the number of QTL detected ranged from three to five in each analysis. In DH180 population, the number of QTL identified varied from three to six in each analysis. A number of common QTL were found between the replicates of each population. Five common QTL were identified between these populations. The markers linked to these QTL are now available for marker assisted selection.