Nested association mapping of important agronomic traits in three interspecific soybean populations

Beche, Eduardo; Gillman, Jason D.; Song, Qijian; Nelson, Randall L.; Beissinger, Tim; Decker, Jared E.; Shannon, Grover; Scaboo, Andrew

doi:10.1007/s00122-019-03529-4

Cited by 14 publications

(10 citation statements)

References 87 publications

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“…4 ; Table 4 ), whereas only two QTL peaks were detected in pop3 in Chr.11 and 18 (data not shown) through the linkage analysis. These data further corroborate the power of rare allele detection in the NAM analysis as observed with increased detection of trait-associated markers (Yu et al 2008 ; Beche et al 2020 ). The top three significant SNPs for each QTL obtained from the NAM analysis are listed in Table 4 .…”

Section: Resultssupporting

confidence: 83%

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Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations

et al. 2022

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Key message An epistatic interaction between SCN resistance loci rhg1-a and rhg2 in PI 90,763 imparts resistance against virulent SCN populations which can be employed to diversify SCN resistance in soybean cultivars. Abstract With more than 95% of the $46.1B soybean market dominated by a single type of genetic resistance, breeding for soybean cyst nematode (SCN)-resistant soybean that can effectively combat the widespread increase in virulent SCN populations presents a significant challenge. Rhg genes (for Resistance to Heterodera glycines) play a key role in resistance to SCN; however, their deployment beyond the use of the rhg1-b allele has been limited. In this study, quantitative trait loci (QTL) were mapped using PI 90,763 through two biparental F3:4 recombinant inbred line (RIL) populations segregating for rhg1-a and rhg1-b alleles against a SCN HG type 1.2.5.7 (Race 2) population. QTL located on chromosome 18 (rhg1-a) and chromosome 11 (rhg2) were determined to confer SCN resistance in PI 90,763. The rhg2 gene was fine-mapped to a 169-Kbp region pinpointing GmSNAP11 as the strongest candidate gene. We demonstrated a unique epistatic interaction between rhg1-a and rhg2 loci that not only confers resistance to multiple virulent SCN populations. Further, we showed that pyramiding rhg2 with the conventional mode of resistance, rhg1-b, is ineffective against these virulent SCN populations. This highlights the importance of pyramiding rhg1-a and rhg2 to maximize the impact of gene pyramiding strategies toward management of SCN populations virulent on rhg1-b sources of resistance. Our results lay the foundation for the next generation of soybean resistance breeding to combat the number one pathogen of soybean.

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Section: Resultssupporting

confidence: 83%

“…1A). This depicts that the allele frequency in mapping populations primarily contributes to the significance of QTL in NAM analysis (Yu et al 2008 ; Beche et al 2020 ). The NAM analysis further detected an additional QTL on Chr.…”

Section: Resultsmentioning

confidence: 99%

Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations

et al. 2022

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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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“…The total seed weight of the central two rows of each plot was measured by the plot combine Almaco R1 or Almaco SPC-40 (Almaco, Nevada, Iowa). The final grain yield was converted to kg·ha −1 on a 13% moisture basis (Beche et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Improve Soybean Variety Selection Accuracy Using UAV-Based High-Throughput Phenotyping Technology

et al. 2022

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The efficiency of crop breeding programs is evaluated by the genetic gain of a primary trait of interest, e.g., yield, achieved in 1 year through artificial selection of advanced breeding materials. Conventional breeding programs select superior genotypes using the primary trait (yield) based on combine harvesters, which is labor-intensive and often unfeasible for single-row progeny trials (PTs) due to their large population, complex genetic behavior, and high genotype-environment interaction. The goal of this study was to investigate the performance of selecting superior soybean breeding lines using image-based secondary traits by comparing them with the selection of breeders. A total of 11,473 progeny rows (PT) were planted in 2018, of which 1,773 genotypes were selected for the preliminary yield trial (PYT) in 2019, and 238 genotypes advanced for the advanced yield trial (AYT) in 2020. Six agronomic traits were manually measured in both PYT and AYT trials. A UAV-based multispectral imaging system was used to collect aerial images at 30 m above ground every 2 weeks over the growing seasons. A group of image features was extracted to develop the secondary crop traits for selection. Results show that the soybean seed yield of the selected genotypes by breeders was significantly higher than that of the non-selected ones in both yield trials, indicating the superiority of the breeder's selection for advancing soybean yield. A least absolute shrinkage and selection operator model was used to select soybean lines with image features and identified 71 and 76% of the selection of breeders for the PT and PYT. The model-based selections had a significantly higher average yield than the selection of a breeder. The soybean yield selected by the model in PT and PYT was 4 and 5% higher than those selected by breeders, which indicates that the UAV-based high-throughput phenotyping system is promising in selecting high-yield soybean genotypes.

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Nested association mapping of important agronomic traits in three interspecific soybean populations

Cited by 14 publications

References 87 publications

Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations

Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

Improve Soybean Variety Selection Accuracy Using UAV-Based High-Throughput Phenotyping Technology

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