C. G. Meinhardt

Potential of Association Mapping and Genomic Selection to Explore PI 88788 Derived Soybean Cyst Nematode Resistance

The potential of association mapping (AM) and genomic selection (GS) has not yet been explored for investigating resistance to soybean cyst nematode (SCN), the most destructive pest affecting soybean. We genotyped 282 representative accessions from the University of Minnesota soybean breeding program using a genome‐wide panel of 1536 single nucleotide polymorphism (SNP) markers and evaluated plant responses to SCN HG type 0. After adjusting for population structure, AM detected significant signals at two loci corresponding to rhg1 and FGAM1 plus a third locus located at the opposite end of chromosome 18. Our analysis also identified a discontinuous long‐range haplotype of over 600 kb around rhg1 locus associated with resistance to SCN HG type 0. The same phenotypic and genotypic datasets were then used to access GS accuracy for prediction of SCN resistance in the presence of major genes through a sixfold cross‐validation study. Genomic selection using the full marker set produced average prediction accuracy ranging from 0.59 to 0.67 for SCN resistance, significantly more accurate than marker‐assisted selection (MAS) strategies using two rhg1‐associated DNA makers. Reducing the number of markers to 288 SNPs in the GS training population had little effect on genomic prediction accuracy. This study demonstrates that AM can be an effective genomic tool for identifying genes of interest in diverse germplasm. The results also indicate that improved MAS and GS can enhance breeding efficiency for SCN resistance in existing soybean improvement programs.

Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean

BackgroundBi-parental mapping populations have been commonly utilized to identify and characterize quantitative trait loci (QTL) controlling resistance to soybean cyst nematode (SCN, Heterodera glycines Ichinohe). Although this approach successfully mapped a large number of SCN resistance QTL, it captures only limited allelic diversity that exists in parental lines, and it also has limitations for genomic resolution. In this study, a genome-wide association study (GWAS) was performed using a diverse set of 553 soybean plant introductions (PIs) belonging to maturity groups from III to V to detect QTL/genes associated with SCN resistance to HG Type 0.ResultsOver 45,000 single nucleotide polymorphism (SNP) markers generated by the SoySNP50K iSelect BeadChip (http//www.soybase.org) were utilized for analysis. GWAS identified 14 loci distributed over different chromosomes comprising 60 SNPs significantly associated with SCN resistance. Results also confirmed six QTL that were previously mapped using bi-parental populations, including the rhg1 and Rhg4 loci. GWAS identified eight novel QTL, including QTL on chromosome 10, which we have previously mapped by using a bi-parental population. In addition to the known loci for four simple traits, such as seed coat color, flower color, pubescence color, and stem growth habit, two traits, like lodging and pod shattering, having moderately complex inheritance have been confirmed with great precision by GWAS.ConclusionsThe study showed that GWAS can be employed as an effective strategy for identifying complex traits in soybean and for narrowing GWAS-defined genomic regions, which facilitates positional cloning of the causal gene(s).

Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding.

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a serious soybean pest. The use of resistant cultivars is an effective approach for preventing yield loss. In this study, 19,652 publicly available soybean accessions that were previously genotyped with the SoySNP50K iSelect BeadChip were used to evaluate the phylogenetic diversity of SCN resistance genes Rhg1 and Rhg4 in an attempt to identify novel sources of resistance. The sequence information of soybean lines was utilized to develop KASPar (KBioscience Competitive Allele-Specific PCR) assays from single nucleotide polymorphisms (SNPs) of Rhg1, Rhg4, and other novel quantitative trait loci (QTL). These markers were used to genotype a diverse set of 95 soybean germplasm lines and three recombinant inbred line (RIL) populations. SNP markers from the Rhg1 gene were able to differentiate copy number variation (CNV), such as resistant-high copy (PI 88788-type), low copy (Peking-type), and susceptible-single copy (Williams 82) numbers. Similarly, markers for the Rhg4 gene were able to detect Peking-type (resistance) genotypes. The phylogenetic information of SCN resistance loci from a large set of soybean accessions and the gene/QTL specific markers that were developed in this study will accelerate SCN resistance breeding programs.

Wheat (Triticum aestivum L.) cultivar selection affects double-crop and relay-intercrop soybean (Glycine max L.) response on claypan soils.

Field research (2003–2005) evaluated the effect of wheat row spacing (19 and 38 cm) and cultivar on double-cropped (DC) soybean response, 38-cm wheat on relay-intercrop (RI) response, and wheat cultivar selection on gross margins of these cropping systems. Narrow-row wheat increased grain yield 460 kg h a − 1 , light interception (LI) 7%, and leaf area index (LAI) 0.5 compared to wide rows, but did not affect DC soybean yield. High yielding wheat (P25R37) with greater LI and LAI produced lower (330 kg  h a − 1 ) soybean yields in an RI system than a low yielding cultivar (Ernie). Gross margins were

Foliar Boron and Pyraclostrobin Effects on Corn Yield

267  h a − 1 greater when P25R37 was RI with H431 Intellicoat (ITC) soybean compared to Ernie. Gross margins were similar for monocrop H431 non-coated (NC) or ITC soybean, P25R37 in 19- or 38-cm rows with DC H431 NC soybean, and P25R37 in 38-cm rows with RI H431 ITC soybean in the absence of an early fall frost.