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.

Soybean [Glycine max (L.) Merr.] is primarily grown as a source of protein and oil. A quantitative trait locus (QTL) controlling seed protein concentration was previously mapped to linkage group (LG) I of soybean. The objectives of this study were to fine map the QTL and to determine if additional recombination could reduce the inverse phenotypic relationship between seed protein concentration and yield and oil concentration. The fine mapping was done with two sets of backcross populations that were tested in the field and with genetic markers. These populations were developed by the introgression of a high protein allele from the Glycine soja Sieb and Zucc. plant introduction (PI) 468916 into the genetic background of the breeding line A81–356022. The first set (Set 1) included three populations of backcross‐four (BC4) lines, and the second set (Set 2) included four populations of BC5 lines. The populations segregated for different segments of the genomic region where the QTL maps. Tests of the two sets of populations resulted in the localization of the QTL for protein and oil to a 3‐cM interval between the simple sequence repeat (SSR) marker Satt239 and the amplified fragment length polymorphism (AFLP) marker ACG9b. The results from the agronomic trait evaluations were inconsistent, making it difficult to definitively conclude whether the protein QTL controls these other traits through pleiotropy.

SummaryRecombination affects the fate of alleles in populations by imposing constraints on the reshuffling of genetic information. Understanding the genetic basis of these constraints is critical for manipulating the recombination process to improve the resolution of genetic mapping, and reducing the negative effects of linkage drag and deleterious genetic load in breeding. Using sequence‐based genotyping of a wheat nested association mapping (NAM) population of 2,100 recombinant inbred lines created by crossing 29 diverse lines, we mapped QTL affecting the distribution and frequency of 102 000 crossovers (CO). Genome‐wide recombination rate variation was mostly defined by rare alleles with small effects together explaining up to 48.6% of variation. Most QTL were additive and showed predominantly trans‐acting effects. The QTL affecting the proximal COs also acted additively without increasing the frequency of distal COs. We showed that the regions with decreased recombination carry more single nucleotide polymorphisms (SNPs) with possible deleterious effects than the regions with a high recombination rate. Therefore, our study offers insights into the genetic basis of recombination rate variation in wheat and its effect on the distribution of deleterious SNPs across the genome. The identified trans‐acting additive QTL can be utilized to manipulate CO frequency and distribution in the large polyploid wheat genome opening the possibility to improve the efficiency of gene pyramiding and reducing the deleterious genetic load in the low‐recombining pericentromeric regions of chromosomes.

that Race 3 SCN resistance in PI 88788 is inherited by three genes, with one recessive and two dominant. The Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is genetic evidence indicates that one of the dominant genes one of the most destructive soybean [Glycine max (L.) Merr.] pests is at a previously unreported locus which was designated worldwide. The most common source of SCN resistance used in soybean breeding in the northern USA is PI 88788. Previous research Rhg5 (Rao Arelli, 1994) the second gene is Rhg4, which has shown that PI 88788 carries a major quantitative trait locus (QTL) maps close to the i gene (Matson and Williams, 1965), conferring SCN resistance on linkage group (LG) G, which is believed and the recessive gene is rhg2. Genetic mapping efforts to be rhg1. The objective of our research was to map and confirm have since shown that PI 88788 has a major QTL on additional SCN resistance QTL in Bell, a cultivar with resistance LG G (Concibido et al., 1997), and a second minor QTL from PI 88788. One hundred four F 4 -derived lines (F 4 population) on LG C2 (Diers et al., 1997a). The QTL on LG G maps developed from crossing the cultivars Bell and Colfax were tested for to the same region where a major resistance locus was associations between 54 molecular markers and resistance to SCN mapped in PI 437654 (Webb et al., 1995), Peking, PI populations PA3 (HG type 7, race 3) and PA14 (HG type 1.3.5.6.7, 90763, PI 89772, and PI 209332 (Concibido et al., 1997; race 14). Three populations of near isogenic lines (NILs) were devel-Concibido et al., 1996; Yue et al., 2001). The resistance oped from F 4 plants heterozygous for a region on LG J where a significant QTL was identified in the F 4 population. The NIL popula-gene in this region has been designated rhg1 in the tions were tested with genetic markers and also for resistance to both literature and Cregan et al. (1999b) reported a linkage SCN populations. In the F 4 population, SCN resistance QTL were of 0.4 centimorgans (cM) between the simple sequence identified at both rhg1 and on LG J. The LG J QTL was confirmed repeat (SSR) marker Satt309 and rhg1 in crosses with in NIL populations and was given the confirmed QTL designation Peking and PI 209332 as sources of SCN resistance. cqSCN-003. The effect of cqSCN-003 was diminished in the NIL Although many QTL have been mapped in soybean, populations compared to the F 4 population. This was at least partially few have been confirmed in additional populations in the result of segregation distortion in the F 4 population between the the same or different genetic backgrounds. The confirregion containing rhg1 and the region containing cqSCN-003. These mation of QTL after initial mapping is a critical step results show the importance of verifying QTL in confirmation populabefore the selection of the QTL with markers in breedtions to estimate accurately their effects.ing programs. Near isogenic line populations are particularly useful for QTL confirmation because they are developed to segregate for QTL ...

Tan spot, caused by Pyrenophora tritici-repentis, is a serious foliar disease of wheat (Triticum aestivum) in North America. Control of tan spot through management practices and fungicide application is possible; however, the use of resistant varieties is the most effective and economical means of controlling tan spot. This study was conducted to determine the disease reaction of 126 elite hard red spring, white, and durum wheat varieties and advanced breeding lines collected from the northern Great Plains of the United States and Canada to individual races/toxins of P. tritici-repentis. Seedling evaluation of the 126 genotypes was done under controlled environmental conditions with virulent races 2, 3, and 5 of P. tritici-repentis and toxins Ptr ToxA and Ptr ToxB. Based on disease reactions, two resistant varieties and two advanced breeding lines adapted to the northern Great Plains were found to be resistant to all the races and insensitive to the toxins tested. Additionally, six genetically diverse lines/varieties were identified to be resistant to tan spot; however, these sources may not be well adapted to the northern Great Plains. These results suggest that the wheat germ plasm contains a broad genetic base for resistance to the most prevalent races of P. tritici-repentis in North America, and the resistant sources identified in this study may be utilized in wheat breeding programs to develop tan spot resistant varieties.