Dadong Zhang

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

Quantitative trait loci for aluminum resistance in Chinese wheat landrace FSW

Aluminum (Al) toxicity is a major constraint for wheat production in acid soils worldwide. Chinese landrace FSW demonstrates a high level of Al resistance. A population of recombinant inbred lines (RILs) was developed from a cross between FSW and an Al-sensitive Chinese line, ND35, using single seed descent, to map quantitative trait loci (QTLs) for Al resistance. Wheat reaction to Al stress was measured by net root growth (NRG) in a nutrient solution culture containing Al3+ and hematoxylin staining score (HSS) of root after Al stress. After 1,437 simple sequence repeats (SSRs) were screened using bulk segregant analysis, three QTLs were identified to control Al resistance in FSW. One major QTL (Qalt.pser-4DL) was mapped on chromosome 4DL that co-segregated with Xups4, a marker for the promoter of the Al-activated malate transporter (ALMT1) gene. The other two QTLs (Qalt.pser-3BL, Qalt.pser-2A) were located on chromosomes 3BL and 2A, respectively. Together, the three QTLs accounted for up to 81.9% of the phenotypic variation for HSS and 78.3% of the variation for NRG. The physical positions of flanking markers for Qalt.pser-4DL and Qalt.pser-3BL were determined by analyzing these markers in corresponding nulli-tetrasomic, ditelosomic, and 3BL deletion lines of Chinese Spring. Qalt.pser-3BL is a novel QTL with a major effect on Al resistance discovered in this study. The two major QTLs on 4DL and 3BL demonstrated an additive effect. The SSR markers closely linked to the QTLs have potential to be used for marker-assisted selection (MAS) to improve Al resistance of wheat cultivars in breeding programs.

Association Analysis of Stem Rust Resistance in U.S. Winter Wheat

Stem rust has become a renewed threat to global wheat production after the emergence and spread of race TTKSK (also known as Ug99) and related races from Africa. To elucidate U.S. winter wheat resistance genes to stem rust, association mapping was conducted using a panel of 137 lines from cooperative U.S. winter wheat nurseries from 2008 and simple sequence repeat (SSR) and sequence tagged site (STS) markers across the wheat genome. Seedling infection types were evaluated in a greenhouse experiment using six U.S. stem rust races (QFCSC, QTHJC, RCRSC, RKQQC, TPMKC and TTTTF) and TTKSK, and adult plant responses to bulked U.S. races were evaluated in a field experiment. A linearization algorithm was used to convert the qualitative Stakman scale seedling infection types for quantitative analysis. Association mapping successfully detected six known stem rust seedling resistance genes in U.S. winter wheat lines with frequencies: Sr6 (12%), Sr24 (9%), Sr31 (15%), Sr36 (9%), Sr38 (19%), and Sr1RSAmigo (8%). Adult plant resistance gene Sr2 was present in 4% of lines. SrTmp was postulated to be present in several hard winter wheat lines, but the frequency could not be accurately determined. Sr38 was the most prevalent Sr gene in both hard and soft winter wheat and was the most effective Sr gene in the adult plant field test. Resistance to TTKSK was associated with nine markers on chromosome 2B that were in linkage disequilibrium and all of the resistance was attributed to the Triticum timopheevii chromosome segment carrying Sr36. Potential novel rust resistance alleles were associated with markers Xwmc326-203 on 3BL, Xgwm160-195 and Xwmc313-225 on 4AL near Sr7, Xgwm495-182 on 4BL, Xwmc622-147 and Xgwm624-146 on 4DL, and Xgwm334-123 on 6AS near Sr8. Xwmc326-203 was associated with adult plant resistance to bulked U.S. races and Xgwm495-182 was associated with seedling resistance to TTKSK.

Identification of new sources of aluminum resistance in wheat

Aluminum (Al) toxicity is a major constraint for wheat production in acidic soils. An Al resistance gene on chromosome 4DL that traces to Brazilian wheat has been extensively studied, and can provide partial protection from Al damage. To identify potentially new sources of Al resistance, 590 wheat accessions, including elite wheat breeding lines from the United States and other American and European countries, landraces and commercial cultivars from East Asia, and synthetic wheat lines from CIMMYT, Mexico, were screened for Al resistance by measuring relative root elongation in culture with a nutrient solution containing Al, and by staining Al-stressed root tips with hematoxylin. Eighty-eight wheat accessions demonstrated at least moderate resistance to Al toxicity. Those selected lines were subjected to analysis of microsatellite markers linked to an Al resistance gene on 4DL and a gene marker for the Al-activated malate transporter (ALMT1) locus. Many of the selected Al-resistant accessions from East Asia did not have the Al-resistant marker alleles of ALMT1, although they showed Al resistance similar to the US Al-resistant cultivar, Atlas 66. Most of the cultivars derived from Jagger and Atlas 66 have the Al-resistant marker alleles of ALMT1. Cluster analysis separated the selected Al-resistant germplasm into two major clusters, labeled as Asian and American–European clusters. Potentially new germplasm of Al resistance different from those derived from Brazil were identified. Further investigation of Al resistance in those new germplasms may reveal alternative Al-resistance mechanisms in wheat.

Fusarium-Damaged Kernels and Deoxynivalenol in Fusarium-Infected U.S. Winter Wheat

Fusarium head blight (FHB) is a devastating disease that threatens wheat (Triticum aestivum) production in many areas worldwide. FHB infection results in Fusarium-damaged kernels (FDK) and deoxynivalenol (DON) that dramatically reduce grain yield and quality. More effective and accurate disease evaluation methods are imperative for successful identification of FHB-resistant sources and selection of resistant cultivars. To determine the relationships among different types of resistance, 363 (74 soft and 289 hard) U.S. winter wheat accessions were repeatedly evaluated for FDK and DON concentration in greenhouse and field experiments. Single-kernel near-infrared (SKNIR)-estimated FDK and DON were compared with visually estimated FDK and gas chromatography-mass spectroscopy-estimated DON. Significant correlations were detected between percentage of symptomatic spikelets and visual FDK in the greenhouse and field, although correlations were slightly lower in the field. High correlation coefficients also were observed between visually scored FDK and SKNIR-estimated FDK (0.72, P < 0.001) and SKNIR-estimated DON (0.68, P < 0.001); therefore, both visual scoring and SKNIR methods are useful for estimating FDK and DON in breeding programs.

Effective marker alleles associated with type 2 resistance to Fusarium head blight infection in fields

Molecular markers associated with known quantitative trait loci (QTLs) for type 2 resistance to Fusarium head blight (FHB) in bi-parental mapping population usually have more than two alleles in breeding populations. Therefore, understanding the association of each allele with FHB response is particularly important to marker-assisted enhancement of FHB resistance. In this paper, we evaluated FHB severities of 192 wheat accessions including landraces and commercial varieties in three field growing seasons, and genotyped this panel with 364 genome-wide informative molecular markers. Among them, 11 markers showed reproducible marker-trait association (p < 0.05) in at least two experiments using a mixed model. More than two alleles were identified per significant marker locus. These alleles were classified into favorable, unfavorable and neutral alleles according to the normalized genotypic values. The distributions of effective alleles at these loci in each wheat accession were characterized. Mean FHB severities increased with decreased number of favorable alleles at the reproducible loci. Chinese wheat landraces and Japanese accessions have more favorable alleles at the majority of the reproducible marker loci. FHB resistance levels of varieties can be greatly improved by introduction of these favorable alleles and removal of unfavorable alleles simultaneously at these QTL-linked marker loci.

Development and validation of diagnostic markers for Fhb1 region, a major QTL for Fusarium head blight resistance in wheat

Key messageFunctional markers were developed based on the critical sequence deletion of TaHRC in the Fhb1 region and validated to be diagnostic in a worldwide wheat collection.AbstractWheat Fusarium head blight (FHB) is a devastating disease in wheat and barley worldwide. Growing FHB-resistant cultivars is an effective strategy to minimize FHB damage in wheat production. Fhb1 is a quantitative trait locus for FHB resistance with the largest effect on disease severity identified to date. With this study, we developed diagnostic DNA markers for Fhb1 by comparing the genomic sequences in Fhb1 region between near-isogenic lines contrasting in Fhb1 alleles and phenotypic effects of the markers. Two markers were developed based on a deletion mutation in an gene encoding a putative histidine-rich calcium-binding protein (TaHRC) and validated in different types of populations. Haplotype or sequence analyses of the two markers in the three sets of diversity panels demonstrated that they are diagnostic for Fhb1, and superior to all previously used markers in selection accuracy. They also have the advantages of low cost, easy assay, and are suitable for breeding programs with either high- or low-throughput marker laboratories.