Hussein Abdel-Haleem

Transcriptomic changes due to water deficit define a general soybean response and accession-specific pathways for drought avoidance

BackgroundAmong abiotic stresses, drought is the most common reducer of crop yields. The slow-wilting soybean genotype PI 416937 is somewhat robust to water deficit and has been used previously to map the trait in a bi-parental population. Since drought stress response is a complex biological process, whole genome transcriptome analysis was performed to obtain a deeper understanding of the drought response in soybean.ResultsContrasting data from PI 416937 and the cultivar ‘Benning’, we developed a classification system to identify genes that were either responding to water-deficit in both genotypes or that had a genotype x environment (GxE) response. In spite of very different wilting phenotypes, 90% of classifiable genes had either constant expression in both genotypes (33%) or very similar response profiles (E genes, 57%). By further classifying E genes based on expression profiles, we were able to discern the functional specificity of transcriptional responses at particular stages of water-deficit, noting both the well-known reduction in photosynthesis genes as well as the less understood up-regulation of the protein transport pathway. Two percent of classifiable genes had a well-defined GxE response, many of which are located within slow-wilting QTLs. We consider these strong candidates for possible causal genes underlying PI 416937’s unique drought avoidance strategy.ConclusionsThere is a general and functionally significant transcriptional response to water deficit that involves not only known pathways, such as down-regulation of photosynthesis, but also up-regulation of protein transport and chromatin remodeling. Genes that show a genotypic difference are more likely to show an environmental response than genes that are constant between genotypes. In this study, at least five genes that clearly exhibited a genotype x environment response fell within known QTL and are very good candidates for further research into slow-wilting.

Identification of QTLs associated with limited leaf hydraulic conductance in soybean

Soybean (Glycine max (L.) Merr.) genotype PI 416937 has been identified as expressing a ‘slow-wilting’ phenotype in the field and this has been traced to a low hydraulic conductance in its leaves. The transpiration rate of de-rooted shoots of this genotype has been found to be insensitive to the aquaporin inhibitor silver nitrate compared to elite cultivars which are silver nitrate sensitive. These results indicated that PI 416937 might have a unique aquaporin population. The objective of this study was to determine if QTLs could be identified that are associated with the lack of sensitivity in PI 416937 to silver. To identify the genomic locations and genetic bases of this trait, a recombinant inbred line population was derived from a mating between PI 416937 and the cultivar ‘Benning’. The RILs were all phenotyped for their response to the silver inhibitor and the results were subjected to a QTL analysis. Four QTL were identified as putatively associated with the silver response (qSV). These QTL explained from 17.7 to 24.7% of the phenotypic variation with qSV_Gm12 explaining the greatest amount of phenotypic variation. The qSV_Gm03 and qSV_Gm10 QTL inherited their positive alleles from PI 416937, while qSV_Gm05 and qSV_Gm12 inherited their favorable alleles from Benning. Co-localized silver nitrate response QTL with other morpho–physiological traits could help to explain soybean plant’s ability to tolerate water-deficit stress.

Genetic Architecture of Novel Traits in the Hopi Sunflower

Following domestication, crop lineages typically undergo diversification either to adapt to disparate habitats or to fill novel agricultural roles. This process has produced the numerous varieties found in modern-day crop germplasm collections. Here, we mapped quantitative trait loci (QTLs) underlying unique traits in the Hopi sunflower, a primitive, Native American domesticate. These traits included a variety of achene (i.e., single-seeded fruit) characters as well as the extremely late flowering time of the Hopi sunflower. Composite interval mapping identified 42 QTLs underlying the 12 traits of interest. Although these QTLs were found on 10 of the 17 sunflower linkage groups, strong genetic correlations were evidenced by the clustering of QTLs across traits in certain genomic regions. The number of QTLs per trait ranged from 2 to 6, and the average QTL explained 14.7% of the variance (range: 2.5-46.9%). The apparent contribution of epistasis was minor, as has previously been observed for domestication-related traits. Unlike typical domestication-related traits in sunflower, the traits under consideration here exhibited a relatively simple genetic basis, with 2 QTL clusters being largely responsible for the unique characteristics of the Hopi sunflower. Based on the rarity of these traits in domesticated sunflower, it would appear that they evolved within the Hopi lineage following domestication. The simple genetic architecture of these traits may be a by-product of genetic constraints imposed by the genetically complex nature of domestication-related traits in sunflower, with the large number of domestication-related QTLs limiting the fraction of the genome that is available for subsequent diversification.

Quantitative trait loci for dry matter digestibility and particle size traits in two-rowed × six-rowed barley population

More than half of the barley grown in the USA is used for livestock feed, with the remaining stocks diverted for human food and malting purposes. The use of barley grain as a major source of cattle feed has been criticized because of its rapid digestion in the rumen, which can result in digestive disorders in cattle. In sacco dry matter digestibility (ISDMD) and particle size (PS) after dry rolling have been found to play a role in the feedlot performance of barley as a feed grain. Reducing the rate of ISDMD is predicted to result in significantly improved animal health and average daily gain. A recombinant inbred line population derived from a cross between a high ISDMD, two-rowed barley cultivar (Valier) and a six-rowed Swiss landrace line (PI370970) exhibiting far slower ISDMD has been developed for studying the underlying genetic locations and mechanisms of these traits. To detect associated quantitative trait loci (QTLs), we collected and analyzed data from irrigated and rain-fed environments. A significant negative correlation was observed between ISDMD and PS. High heritability estimates for ISDMD and PS suggest that early selection for these traits during breeding would be achievable. Four QTLs were identified on chromosomes 2H, 6H, and 7H, explaining 73–85% of ISDMD phenotypic variation, while three QTLs on 2H and 7H were associated with variation in PS and explained 58–77% of its variation. A major QTL on chromosome 2H tightly linked to the morphology-modifying gene vrs1 was found to dramatically control 35–62% of the phenotypic variation of ISDMD and 26–53% of that of PS. The impact of the vrs1 locus on ISDMD was validated in two populations representing different genetic backgrounds. Our results suggest that it may also be advantageous to simultaneously overlap these QTLs around the vrs1 locus.

Quantitative trait loci of acid detergent fiber and grain chemical composition in hulled × hull-less barley population

Cultivated barley is the major livestock feed grain in the Northern Plains and Northwestern United States due to the fact that its short growing season and limited rainfall limit the planting and production of corn. Starch and fiber content play a significant role in feedlot performance of animals raised on barley feed. To study the underlying genetic locations and mechanisms for these traits, a recombinant inbred line population was derived from a cross between the hulled barley cultivar Valier and a hull-less Swiss landrace line, PI370970. Valier has a high acid detergent fiber content (ADF) and low starch and protein while PI370970 contains low ADF and high starch and protein content. To detect associated QTLs, data were collected and analyzed from irrigated and rain-fed environments. A total of 30 main effect QTLs and four epistatic QTLs were identified which conditioned ADF, starch and protein content under rain-fed, irrigated and combined analyses. These QTLs were located on chromosomes 2H, 3H, 5H, 6H and 7H. Major ADF and starch QTL were identified on chromosome 7H near the nud locus (the locus controlling hulled vs. hull-less caryopsis). High heritability estimates for both ADF and starch content suggest that early selection for these traits during breeding would be productive. Low ADF-QTL were independently verified in a second population in a different genetic background.

An R package for SNP marker-based parent-offspring tests

BackgroundWith the advancement of genotyping technologies, whole genome and high-density SNP markers have been widely used for genotyping of mapping populations and for characterization of germplasm lines in many crops. Before conducting SNP data analysis, it is necessary to check the individuals to ensure the integrity of lines for further data analysis.ResultsWe have developed an R package to conduct a parent-offspring test of individuals which are genotyped with a fixed set of SNP markers for further genetic studies. The program uses monomorphic SNP loci between parents and their progeny genotypes to calculate the similarity between each offspring and their parents. Based on the similarity of parents and individual offspring, the users can determine the threshold level for the individuals to be included for further data analysis. We used an F5-derived soybean population of ‘5601T’ x PI 157440 that was genotyped with 1,536 SNPs to illustrate the procedure and its application.ConclusionsThe R package ‘ParentOffspring’ coupled with the available SNP genotyping platforms could be used to detect the possible variants in a specific cross, as well as the potential errors in sample handling and genotyping processes. It can be used in any crop which is genotyped with a fixed set of SNP markers.