Brett F. Carver

Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.).

BackgroundSingle nucleotide polymorphisms (SNPs) are ideally suited for the construction of high-resolution genetic maps, studying population evolutionary history and performing genome-wide association mapping experiments. Here, we used a genome-wide set of 1536 SNPs to study linkage disequilibrium (LD) and population structure in a panel of 478 spring and winter wheat cultivars (Triticum aestivum) from 17 populations across the United States and Mexico.ResultsMost of the wheat oligo pool assay (OPA) SNPs that were polymorphic within the complete set of 478 cultivars were also polymorphic in all subpopulations. Higher levels of genetic differentiation were observed among wheat lines within populations than among populations. A total of nine genetically distinct clusters were identified, suggesting that some of the pre-defined populations shared significant proportion of genetic ancestry. Estimates of population structure (FST) at individual loci showed a high level of heterogeneity across the genome. In addition, seven genomic regions with elevated FST were detected between the spring and winter wheat populations. Some of these regions overlapped with previously mapped flowering time QTL. Across all populations, the highest extent of significant LD was observed in the wheat D-genome, followed by lower LD in the A- and B-genomes. The differences in the extent of LD among populations and genomes were mostly driven by differences in long-range LD ( > 10 cM).ConclusionsGenome- and population-specific patterns of genetic differentiation and LD were discovered in the populations of wheat cultivars from different geographic regions. Our study demonstrated that the estimates of population structure between spring and winter wheat lines can identify genomic regions harboring candidate genes involved in the regulation of growth habit. Variation in LD suggests that breeding and selection had a different impact on each wheat genome both within and among populations. The higher extent of LD in the wheat D-genome versus the A- and B-genomes likely reflects the episodes of recent introgression and population bottleneck accompanying the origin of hexaploid wheat. The assessment of LD and population structure in this assembled panel of diverse lines provides critical information for the development of genetic resources for genome-wide association mapping of agronomically important traits in wheat.

Wheat : science and trade

WHEAT SCIENCE AND TRADE provides an in depth review of wheat biology, production, breeding, processing, and trade. The book is organized in four sections. “Making of a Wheat Plant” reviews domestication, evolution, development, and molecular control of l owering. “Making of a Wheat Crop” considers management, diseases, pests, and weeds. In “Making of a Wheat Cultivar,” crop improvement is examined across the spectrum from conventional breeding, to creation of synthetic wheats, to transgenic approaches. The i nal section, “Making of a Wheat Industry,” looks at grain quality, novel uses, and marketing. The 23 chapters were authored by experts from 10 countries, notably the U.S., Australia, and Canada. The content is clearly written and current through 2007, with a few citations from 2008. A notable feature is the extensive inclusion of information from molecular biology. As with any compendium, issues can be raised concerning balance and completeness of coverage. Chapters varied in whether the content primarily had a global or U.S. focus. In many cases, it would have been interesting to compare among major wheat regions, especially China, India, and Pakistan. The review of physiology was largely limited to development and control of l owering. Viral diseases are only mentioned in relation to vectors and interactions with other diseases. The chapter “Grain yield improvement in water-limited environments” dealt largely with breeding strategies, yet it preceded the chapter that introduced conventional breeding. The material largely employs a graduate-level terminology for phytopathology, genetics, molecular biology, and biochemistry. Individual chapters might be suitable as course material, but the main use of the book would seem to be as introductory or refresher material for the wheat research community. Obvious cases would be for a researcher recently assigned to work on wheat or a researcher who feels a need to review their i eld to understand how modern technologies, especially from molecular biology, might af ect their work. An unresolved issue is whether such a compendium still has value in an era when knowledge is evolving rapidly. The Internet provides authors the ability to update information as needed and to rely extensively on color diagrams and photos or even provide animation or videos. However, the Internet still lacks the quality of editing that is apparent in Wheat Science and Trade and lags in ease of access if one is fortunate enough to have the right book on the shelf. Of course, this raises a second issue: at

Genetic analysis and selection for wheat yield in drought-stressed and irrigated environments

250, the book is more likely to reside in a central library than on every researcher’s bookshelf. —Jef rey W. White USDAARS-USALARC 21881 N. Cardon Lane Maricopa, AZ 85138, USA jef rey.white@ars.usda.gov

Molecular mapping of a quantitative trait locus for aluminum tolerance in wheat cultivar Atlas 66

SummaryWheat (Triticum aestivum L.) cultivars grown in the southern Great Plains of the U.S.A. are exposed to a wide range of moisture conditions due to large fluctuations in the amount and frequency of rainfall. Yield stability under those conditions is therefore a desirable trait for wheat breeders. Our primary objective was to quantify various genetic parameters for grain production in drought-stressed and irrigated environments. We also attempted to predict and measure yield responses when selection is practiced in either drought-stressed or irrigated environments, or both. Seventy F2-derived lines from the cross, TAM W-101/Sturdy, were evaluated at Goodwell, OK, under irrigated and naturally drought-stressed conditions in 1987 and 1988. Genetic variance and heritability estimates were higher in the irrigated environment than in the drought-stressed environment. The genetic correlation coefficient for yields in the two environments was 0.20±0.16, indicating that selection of widely adapted genotypes requires testing in both environments. Based on the genetic variance/covariance structure of this particular population, the linear index which maximized the combined expected gain in both environments was 0.66Y1 + 0.34Y2, in which Y1 and Y2 are yields in the irrigated and drought-stressed environments. This index is not expected to apply across all populations; rather, it further supports the hypothesis that testing in either environment alone (drought stressed or irrigated) may not be most effective for increasing either mean productivity or yield under drought stress.

Genetic Diversity, Population Structure, and Linkage Disequilibrium in U.S. Elite Winter Wheat

Genetic improvement of aluminum (Al) tolerance is one of the cost-effective solutions to improve wheat (Triticum aestivum) productivity in acidic soils. The objectives of the present study were to identify quantitative trait loci (QTL) for Al-tolerance and associated PCR-based markers for marker-assisted breeding utilizing cultivar Atlas 66. A population of recombinant inbred lines (RILs) from the cross Atlas 66/Century was screened for Al-tolerance by measuring root-growth rate during Al treatment in hydroponics and root response to hematoxylin stain of Al treatment. After 797 pairs of SSR primers were screened for polymorphisms between the parents, 131 pairs were selected for bulk segregant analysis (BSA). A QTL analysis based on SSR markers revealed one QTL on the distal region of chromosome arm 4DL where a malate transporter gene was mapped. This major QTL accounted for nearly 50% of the phenotypic variation for Al-tolerance. The SSR markers Xgdm125 and Xwmc331 were the flanking markers for the QTL and have the potential to be used for high-throughput, marker-assisted selection in wheat-breeding programs.

Mapping quantitative trait loci for quality factors in an inter-class cross of US and Chinese wheat

Information on genetic diversity and population structure of elite wheat (Triticum aestivum L.) breeding lines promotes effective use of genetic resources. We analyzed 205 elite wheat breeding lines from major winter wheat breeding programs in the USA using 245 markers across the wheat genomes. This collection showed a high level of genetic diversity as reflected by allele number per locus (7.2) and polymorphism information content (0.54). However, the diversity of U.S. modern wheat appeared to be lower than previously reported diversity levels in worldwide germplasm collections. As expected, this collection was highly structured according to geographic origin and market class with soft and hard wheat clearly separated from each other. Hard wheat accessions were further divided into three subpopulations. Linkage disequilibrium (LD) was primarily distributed around centromere regions. The mean genome‐wide LD decay estimate was 10 cM (r2 > 0.1), although the extent of LD was highly variable throughout the genome. Our results on genetic diversity of different gene pools and the distribution of LD facilitates the effective use of genetic resources for wheat breeding and the choice of marker density in gene mapping and marker‐assisted breeding.

Genetic loci associated with stem elongation and winter dormancy release in wheat

Wheat quality factors are critical in determining the suitability of wheat (Triticum aestivum L.) for end-use product and economic value, and they are prime targets for marker-assisted selection. Objectives of this study were to identify quantitative trait loci (QTLs) that ultimately influence wheat market class and milling quality. A population of 132 F12 recombinant inbred lines (RILs) was derived by single-seed descent from a cross between the Chinese hard wheat line Ning7840 and the soft wheat cultivar Clark and grown at three Oklahoma locations from 2001 to 2003. Milling factors such as test weight (volumetric grain weight, TW), kernel weight (KW), and kernel diameter (KD) and market class factors such as wheat grain protein content (GPC) and kernel hardness index (HI) were characterized on the basis of a genetic map constructed from 367 SSR and 241 AFLP markers covering all 21 chromosomes. Composite interval mapping identified eight QTLs for TW, seven for KW, six for KD, two each for GPC and HI measured by near-infrared reflectance (NIR) spectroscopy, and four for HI measured by single kernel characterization system. Positive phenotypic correlations were found among milling factors. Consistent co-localized QTLs were identified for TW, KW, and KD on the short arms of chromosomes 5A and 6A. A common QTL was identified for TW and KD on the long arm of chromosome 5A. A consistent major QTL for HI peaked at the Pinb-D1 locus on the short arm of chromosome 5D and explained up to 85% of the phenotypic variation for hardness. We identified QTLs for GPC on 4B and the short arm of 3A chromosomes. The consistency of quality factor QTLs across environments reveals their potential for marker-assisted selection.

Genetic trends in winter Wheat yield and test weight under dual-purpose and grain-only management systems

In winter wheat (Triticum aestivum L.), the stem begins to elongate after the vernalization requirement is satisfied during winter and when favorable temperature and photoperiod conditions are attained in spring. In this study, we precisely measured elongation of the first extended internode on 96 recombinant inbred lines of a population that was generated from a cross between two winter wheat cultivars, Jagger (early stem elongation) and 2174 (late stem elongation). We mapped a major locus for stem elongation to the region where VRN-A1 resides in chromosome 5A. Visible assessment of winter dormancy release was concomitantly associated with this locus. VRN1 was previously cloned based on variation in vernalization requirement between spring wheat carrying a dominant Vrn-1 allele and winter wheat carrying a recessive vrn-1 allele. Both of two winter wheat cultivars in this study carry a recessive vrn-A1 allele; therefore, our results suggest that either VRN-A1 might invoke a new regulatory mechanism or a new gene residing close to VRN-A1 plays a regulatory role in winter wheat development. Phenotypic expression of the vrn-A1a allele of Jagger was more sensitive to the year of measurement of stem elongation than that of the vrn-A1b allele of 2174. In addition to QSte.osu.5A, several loci were also found to have minor effects on initial stem elongation of winter wheat. Seventeen of nineteen locally adapted cultivars in the southern Great Plaints contained the vrn-A1b allele. Hence, breeders in this area have inadvertently selected this allele, contributing to later stem elongation and more conducive developmental patterns for grain production.

Quantitative trait loci for aluminum resistance in wheat

Wheat (Triticum aestivum L.) cultivars of the southern Great Plains are traditionally bred in environments managed for grain production only but are commonly grown for the dual-purpose of producing winter forage and grain from the same crop. To what extent grain yield and test weight are consistently expressed in those environments requires investigation relative to long-term attempts to improve them genetically. A historical set of hard red winter (HRW) wheat cultivars was evaluated under grain-only and dual-purpose management systems to compare their agronomic performance and derived estimates of genetic progress. Separate experiments were established for each system featuring whole-plot treatments of a foliar fungicide and split-plot treatments of 12 cultivars. The study was conducted for 3 yr at the Wheat Pasture Res. Ctr. near Marshall, OK. Dual-purpose experiments were generally grazed from November through February. Yield in the grain-only system improved 18.8 kg ha -1 yr -1 , equivalent to 1.3% of the mean yield for Turkey. The rate of progress in the dual-purpose system was significantly lower at 11.3 kg ha -1 yr -1 , equivalent to 0.9% of the mean for Turkey. Management for grazing had a more profound influence on estimates of yield improvement than did management for disease protection. Linear trends in test weight were not evident under either system, nor were cultivar differences influenced by management system consistently across years. Breeding practices should emphasize selection for grain yield in both environments if future progress is to be maximized in both.

Genetic diversity of photosynthetic characters in native populations of Triticum dicoccoides.

Quantitative trait loci (QTL) for wheat resistance to aluminum (Al) toxicity were analyzed using simple sequence repeats (SSRs) in a population of 192 F6 recombinant inbred lines (RILs) derived from a cross between an Al-resistant cultivar, Atlas 66 and an Al-sensitive cultivar, Chisholm. Wheat reaction to Al was measured by relative root growth and root response to hematoxylin stain in nutrient-solution culture. After screening 1,028 SSR markers for polymorphisms between the parents and bulks, we identified two QTLs for Al resistance in Atlas 66. One major QTL was mapped on chromosome 4D that co-segregated with the Al-activated malate transporter gene (ALMT1). Another minor QTL was located on chromosome 3BL. Together, these two QTLs accounted for about 57% of the phenotypic variation in hematoxylin staining score and 50% of the variation in net root growth (NRG). Expression of the minor QTL on 3BL was suppressed by the major QTL on 4DL. The two QTLs for Al resistance in Atlas 66 were also verified in an additional RIL population derived from Atlas 66/Century. Several SSR markers closely linked to the QTLs were identified and have potential to be used for marker-assisted selection (MAS) to improve Al-resistance of wheat cultivars in breeding programs.