Several leaf traits of soybean (Glycine max L. Merr.), including leaf area (LA), leaf shape (LS) and specific leaf weight (SLW) may be related to soybean yield. The objective of this study was to identify novel quantitative trait loci (QTL) for LA, LS and SLW in a recombinant inbred line (RIL) population. The phenotype data were collected in 2011 and 2012 for 93 F7:10 RILs using a randomized complete block design with 2 replicates each year. Five hundred and sixteen single‐nucleotide polymorphism (SNP) markers and the phenotype data were used to detect QTL using single marker analysis (SMA) and composite interval mapping (CIM). Single markers analysis identified 26 QTL for the three traits, of which 17 were novel and the rests were previously reported QTL. Most of these QTL were also identified by CIM. Most QTL reported in this study were in close proximity (<1 cM) of one or more SNP markers. These publicly available SNP markers with close linkage to LA, LS and SLW should be useful for marker‐assisted breeding for these traits.
The objective of this study was to construct a high-density genetic map of soybean (Glycine max L. Merr) using a high-throughput single nucleotide polymorphism (SNP) genotyping on 357 F 7 recombinant inbred lines from a cross of 'Wyandot' 9 PI 567301B. Of 5,403 SNP loci scored from the Infinium BARCSoySNP6K BeadChip array, 2,585 (48 %) were polymorphic between the two parents and subsequently 2,563 SNPs remained after filtering for minor allele frequency, heterozygosity, and missing data. A total of 2,545 SNPs were mapped into 20 linkage groups corresponding to the 20 chromosomes of soybean. The total length of the map was 2,346 cM with 2,213 unique SNP loci with 86 to 162 unique loci per chromosome. Average marker interval ranged from 0.9 to 1.3 cM with an overall mean of 1.1 cM, but 22 marker intervals were still greater than 10 cM. Colinear relationship was observed between genetic (cM) and physical positions (Mb) of SNPs for most of the genome, highlighting the improvements in the updated soybean genome assembly Glyma.Wm82.a2Electronic supplementary material The online version of this article (
The soybean aphid (Aphis glycines Matsumura) is one of the most important insect pests of soybean [Glycine max (L.) Merr.] in North America, and three biotypes of the aphid have been confirmed. Genetic studies of the soybean aphid are needed to determine genetic diversity, movement pattern, biotype distribution and mapping of virulence genes for efficient control of the pest. Simple sequence repeats (SSR) markers are useful for population and classical genetic studies, but few are currently available for the soybean aphid. In this study, we designed primers for 342 genic‐SSR markers from a dataset of more than 102 024 transcript reads generated by 454 GS FLX sequencing of a cDNA library of the soybean aphid. Two hundred forty‐six markers generated PCR products of expected size and 26 were polymorphic among four pooled aphid DNA samples. An additional five markers that were fixed for two alleles among the pooled samples were found to be polymorphic when tested on 96 individual aphids. Sequencing of the PCR products generated by two polymorphic SSR markers revealed that the polymorphisms were strictly because of variations in the SSR repeats among the aphids tested. The genetic diversity among 96 soybean aphids, 24 each from two field collections (South Dakota and Michigan, biotype unknown) and two laboratory colonies [biotype 1 (B1) and biotype 2 (B2)], was assessed with 29 polymorphic SSR markers. These markers discriminated laboratory colonies from field collections and field collections from different states. The genic‐SSR markers developed and validated in this study will be a significant addition to the limited number of SSR markers, mostly genomic‐SSR, currently available for the soybean aphid. These markers will be useful for genetic studies, including population genetics, genetic and QTL mapping, migration and biotype differentiation of the soybean aphid.
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