Registration of Wyandot × PI 567301B Soybean Recombinant Inbred Line Population

Lee, Sung‐Woo; Jun, Tae-Hwan; McHale, Leah K.; Michel, Andrew P.; Dorrance, Anne E.; Song, Qijian; Mian, M. A. Rouf

doi:10.3198/jpr2016.09.0042crmp

Cited by 5 publications

(3 citation statements)

References 41 publications

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“…In 2015, the 621 accessions (Table S1) were planted in three mid-western and one southern locations of the USA [Wooster (OHW15) and Columbus, OH (OHC15), Urbana, IL (IL15) and Plymouth, NC (NC15)] with two replications at each environment in an augmented randomized complete block design (ARCBD). Each replicate within the ARCBD was divided into 4 blocks, which included no more than 196 accessions and four checks: ‘Summit’ (McHale et al 2013 ), ‘Wyandot’ (Lee et al 2017 ; https://mchalelab.cfaes.ohio-state.edu/sites/mchale/files/imce/Wyandot_release_document.pdf ), HR09-397 (a high protein breeding line from USDA-ARS, Wooster, OH) and ‘Prohio’ (Mian et al 2008 ).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV

et al. 2019

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Key message Genomic regions associated with seed protein, oil and amino acid contents were identified by genome-wide association analyses. Geographic distributions of haplotypes indicate scope of improvement of these traits. Abstract Soybean [ Glycine max (L.) Merr.] protein and oil are used worldwide in feed, food and industrial materials. Increasing seed protein and oil contents is important; however, protein content is generally negatively correlated with oil content. We conducted a genome-wide association study using phenotypic data collected from five environments for 621 accessions in maturity groups I–IV and 34,014 markers to identify quantitative trait loci (QTL) for seed content of protein, oil and several essential amino acids. Three and five genomic regions were associated with seed protein and oil contents, respectively. One, three, one and four genomic regions were associated with cysteine, methionine, lysine and threonine content (g kg −1 crude protein), respectively. As previously shown, QTL on chromosomes 15 and 20 were associated with seed protein and oil contents, with both exhibiting opposite effects on the two traits, and the chromosome 20 QTL having the most significant effect. A multi-trait mixed model identified trait-specific QTL. A QTL on chromosome 5 increased oil with no effect on protein content, and a QTL on chromosome 10 increased protein content with little effect on oil content. The chromosome 10 QTL co-localized with maturity gene E2 / GmGIa . Identification of trait-specific QTL indicates feasibility to reduce the negative correlation between protein and oil contents. Haplotype blocks were defined at the QTL identified on chromosomes 5, 10, 15 and 20. Frequencies of positive effect haplotypes varied across maturity groups and geographic regions, providing guidance on which alleles have potential to contribute to soybean improvement for specific regions. Electronic supplementary material The online version of this article (10.1007/s00122-019-03304-5) contains supplementary material, which is available to authorized users.

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Section: Methodsmentioning

confidence: 99%

Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV

et al. 2019

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“…Because South Korean accessions with potential novel Rps genes are also genetically distant from U.S. genotypes (Burnham et al, 2002), the use of these accessions in breeding programs has the potential to expand the diversity of U.S. soybean cultivars. However, expanding the diversity of soybean can often result in the introgression of other yieldlimiting traits; therefore, molecular markers that are associated with the Rps genes are needed (Carter et al, 2004;Lee et al, 2017). This study sought to identify and map new Rps loci in the PIs 407974B and 424487B because they all contained more than one Rps gene.…”

Section: Core Ideasmentioning

confidence: 99%

Identification of resistance loci toward Phytophthora sojae in South Korean soybean plant introductions 407974B and 424487B

et al. 2021

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Phytophthora root and stem rot is a major constraint to soybean [Glycine max (L.) Merr.] production worldwide. Deployment of single dominant Resistance to Phytophthora sojae (Rps) genes are an effective management strategy for this disease. However, due to increasing diversity in P. sojae populations for pathotype, new effective Rps genes are needed. Two recombinant inbred line (RIL) populations, each derived from a cross with Williams (susceptible) and resistant accessions PI 407974B and PI 424487B, were evaluated for resistance with one or more P. sojae pathotypes: OH1 (vir 7), OH4 (vir 1a, 1c, 7), OH7 (vir 1a, 3a, 3c, 4, 5, 6, 7), OH25 (vir 1a, 1b, 1c, 1k, 7), and 1.S.1.1 (1a, 1b, 1k, 2, 3a, 3c, 4, 5, 6, 7, 8). Molecular maps were assembled with BARCSoySNP6K BeadChip, simple‐sequence repeat, and Kompetitive Allele Specific polymerase chain reaction markers. A total of three Rps loci were mapped, one near Rps1 on Chromosome 3 and two near Rps4/6 on chromosome 18. Quantitative trait loci and straight linkage maps confirmed the loci. Resistance to P. sojae pathotypes 1.S.1.1 and/or OH7 was mapped to Chromosome 3 in the PI 407974B RIL population. PI 407974B and PI 424487B RIL populations have Rps loci on chromosome 18 toward OH4 and OH25, respectively, which are near the Rps4/6 region. Although these PIs may have novel Rps genes/alleles and could assist in the deployment and pyramiding of resistance against P. sojae, care should be taken because these may condition defense reactions to some P. sojae pathotypes but not to all.

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“…Cross validation analysis showed that high predictive abilities for protein, oil could be achieved with these markers, while a larger training set size in combination with increased genetic relatedness between training and validation set could further improve predictive ability of seed yield. In addition, the 6K assay has been used to map agronomy traits in nested association mapping populations (Beche et al ., 2020), to estimate population structure, pedigree and LD (Contreras‐Soto et al ., 2017), and characterize the mapping population for registration (Lee et al ., 2017). The assay has been proven useful and efficient by the soybean breeders and geneticists working in the private and public sectors, and the assay was commercialized by Illumina (http://www.illumina.com/areas-of-interest/agrigenomics/consortia.html).…”

Section: Discussionmentioning

confidence: 99%

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

et al. 2020

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The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000-2000 genome-wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARC-SoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.

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Registration of Wyandot × PI 567301B Soybean Recombinant Inbred Line Population

Cited by 5 publications

References 41 publications

Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV

Genome-wide association study of seed protein, oil and amino acid contents in soybean from maturity groups I to IV

Identification of resistance loci toward Phytophthora sojae in South Korean soybean plant introductions 407974B and 424487B

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

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