Genomic prediction of hybrid performance in grain sorghum (Sorghum bicolor L.).

Genomic selection is expected to improve selection efficiency and genetic gain in breeding programs. The objective of this study was to assess the efficacy of predicting the performance of grain sorghum hybrids using genomic information of parental genotypes. One hundred and two public sorghum inbred parents were genotyped using genotyping-by-sequencing. Ninty-nine of the inbreds were crossed to three tester female parents generating a total of 204 hybrids for evaluation at two environments. The hybrids were sorted in to three sets of 77,59 and 68 and evaluated along with two commercial checks using a randomized complete block design in three replications. The sequence analysis generated 66,265 SNP markers that were used to predict the performance of 204 F1 hybrids resulted from crosses between the parents. Both additive (partial model) and additive and dominance (full model) were constructed and tested using various training population (TP) sizes and cross-validation procedures. Increasing TP size from 41 to 163 increased prediction accuracies for all traits. With the partial model, the five-fold cross validated prediction accuracies ranged from 0.03 for thousand kernel weight (TKW) to 0.58 for grain yield (GY) while it ranged from 0.06 for TKW to 0.67 for GY with the full model. The results suggest that genomic prediction could become an effective tool for predicting the performance of sorghum hybrids based on parental genotypes.

QTL mapping of yield components and kernel traits in wheat cultivars TAM 112 and Duster.

In the Southern Great Plains, wheat cultivars have been selected for a combination of outstanding yield and drought tolerance as a long-term breeding goal. To understand the underlying genetic mechanisms, this study aimed to dissect the quantitative trait loci (QTL) associated with yield components and kernel traits in two wheat cultivars `TAM 112' and `Duster' under both irrigated and dryland environments. A set of 182 recombined inbred lines (RIL) derived from the cross of TAM 112/Duster were planted in 13 diverse environments for evaluation of 18 yield and kernel related traits. High-density genetic linkage map was constructed using 5,081 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing (GBS). QTL mapping analysis detected 134 QTL regions on all 21 wheat chromosomes, including 30 pleiotropic QTL regions and 21 consistent QTL regions, with 10 QTL regions in common. Three major pleiotropic QTL on the short arms of chromosomes 2B (57.5 - 61.6 Mbps), 2D (37.1 - 38.7 Mbps), and 7D (66.0 - 69.2 Mbps) colocalized with genes Ppd-B1, Ppd-D1, and FT-D1, respectively. And four consistent QTL associated with kernel length (KLEN), thousand kernel weight (TKW), plot grain yield (YLD), and kernel spike-1 (KPS) (Qklen.tamu.1A.325, Qtkw.tamu.2B.137, Qyld.tamu.2D.3, and Qkps.tamu.6A.113) explained more than 5% of the phenotypic variation. QTL Qklen.tamu.1A.325 is a novel QTL with consistent effects under all tested environments. Marker haplotype analysis indicated the QTL combinations significantly increased yield and kernel traits. QTL and the linked markers identified in this study will facilitate future marker-assisted selection (MAS) for pyramiding the favorable alleles and QTL map-based cloning.

Genome-Wide Association Mapping of Seedling Drought Tolerance in Winter Wheat.

In the southern Great Plains of the United States, winter wheat grown for dual-purpose is often planted early, which puts it at risk for drought stress at the seedling stage in the autumn. To map quantitative trait loci (QTL) associated with seedling drought tolerance, a genome-wide association study (GWAS) was performed on a hard winter wheat association mapping panel. Two sets of plants were planted in the greenhouse initially under well-watered conditions. At the five-leaf stage, one set continued to receive the optimum amount of water, whereas watering was withdrawn from the other set (drought stress treatment) for 14 days to mimic drought stress. Large phenotypic variation was observed in leaf chlorophyll content, leaf chlorophyll fluorescence, shoot length, number of leaves per seedling, and seedling recovery. A mixed linear model analysis detected multiple significant QTL associated with seedling drought tolerance-related traits on chromosomes 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4B, 5A, 5B, 6B, and 7B. Among those, 12 stable QTL responding to drought stress for various traits were identified. Shoot length and leaf chlorophyll fluorescence were good indicators in responding to drought stress because most of the drought responding QTL detected using means of these two traits were also detected in at least two experimental repeats. These stable QTL are more valuable for use in marker-assisted selection during wheat breeding. Moreover, different traits were mapped on several common chromosomes, such as 1B, 2B, 3B, and 6B, and two QTL clusters associated with three or more traits were located at 107-130 and 80-83 cM on chromosomes 2B and 6B, respectively. Furthermore, some QTL detected in this study co-localized with previously reported QTL for root and shoot traits at the seedling stage and canopy temperature at the grain-filling stage of wheat. In addition, several of the mapped chromosomes were also associated with drought tolerance during the flowering or grain-filling stage in wheat. Some significant single-nucleotide polymorphisms (SNPs) were aligned to candidate genes playing roles in plant abiotic stress responses. The SNP markers identified in this study will be further validated and used for marker-assisted breeding of seedling drought tolerance during dual-purpose wheat breeding.

Genome-Wide Association Mapping of Seedling Heat Tolerance in Winter Wheat.

Heat stress during the seedling stage of early-planted winter wheat (Triticum aestivum L.) is one of the most abiotic stresses of the crop restricting forage and grain production in the Southern Plains of the United States. To map quantitative trait loci (QTLs) and identify single-nucleotide polymorphism (SNP) markers associated with seedling heat tolerance, a genome-wide association mapping study (GWAS) was conducted using 200 diverse representative lines of the hard red winter wheat association mapping panel, which was established by the Triticeae Coordinated Agricultural Project (TCAP) and genotyped with the wheat iSelect 90K SNP array. The plants were initially planted under optimal temperature conditions in two growth chambers. At the three-leaf stage, one chamber was set to 40/35°C day/night as heat stress treatment, while the other chamber was kept at optimal temperature (25/20°C day/night) as control for 14 days. Data were collected on leaf chlorophyll content, shoot length, number of leaves per seedling, and seedling recovery after removal of heat stress treatment. Phenotypic variability for seedling heat tolerance among wheat lines was observed in this study. Using the mixed linear model (MLM), we detected multiple significant QTLs for seedling heat tolerance on different chromosomes. Some of the QTLs were detected on chromosomes that were previously reported to harbor QTLs for heat tolerance during the flowering stage of wheat. These results suggest that some heat tolerance QTLs are effective from the seedling to reproductive stages in wheat. However, new QTLs that have never been reported at the reproductive stage were found responding to seedling heat stress in the present study. Candidate gene analysis revealed high sequence similarities of some significant loci with candidate genes involved in plant stress responses including heat, drought, and salt stress. This study provides valuable information about the genetic basis of seedling heat tolerance in wheat. To the best of our knowledge, this is the first GWAS to map QTLs associated with seedling heat tolerance targeting early planting of dual-purpose winter wheat. The SNP markers identified in this study will be used for marker-assisted selection (MAS) of seedling heat tolerance during dual-purpose wheat breeding.

Sorghum Landrace Collections from Cooler Regions of the World Exhibit Magnificent Genetic Differentiation and Early Season Cold Tolerance.

Cold temperature is an important abiotic stress affecting sorghum production in temperate regions. It reduces seed germination, seedling emergence and seedling vigor thus limiting the production of the crop both temporally and spatially. The objectives of this study were (1) to assess early season cold temperature stress response of sorghum germplasm from cooler environments and identify sources of tolerance for use in breeding programs, (2) to determine population structure and marker-trait association among these germplasms for eventual development of marker tools for improving cold tolerance. A total of 136 sorghum accessions from cooler regions of the world were phenotyped for seedling growth characteristics under cold temperature imposed through early planting. The accessions were genotyped using 67 simple sequence repeats markers spanning all ten linkage groups of sorghum, of which 50 highly polymorphic markers were used in the analysis. Genetic diversity and population structure analyses sorted the population into four subpopulations. Several accessions distributed in all subpopulations showed either better or comparable level of tolerance to the standard cold tolerance source, Shan qui red. Association analysis between the markers and seedling traits identified markers Xtxp34, Xtxp88, and Xtxp319 as associated with seedling emergence, Xtxp211 and Xtxp304 with seedling dry weight, and Xtxp20 with seedling height. The markers were detected on chromosomes previously found to harbor QTLs associated with cold tolerance in sorghum. Once validated these may serve as genomic tools in marker-assisted breeding or for screening larger pool of genotypes to identify additional sources of cold tolerance.