Bayesian mapping of quantitative trait loci (QTL) controlling soybean cyst nematode resistant

Arriagada, Osvin; Mora, Freddy; Dellarossa, Joaquín C.; Ferreira, Márcia Flores da Silva; Cervigni, Gerardo Domingo Lucio; Schuster, Ivan

doi:10.1007/s10681-012-0696-y

Cited by 23 publications

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“…Among the 12 QTN (nucleotides) associated with QTL underlying resistance to SCN Hg Type 0, one QTN (rs8050006) was identified on chromosome 8 (Gm 08, LG A2), where a known and major QTL region associated with Rhg4 locus had been commonly reported before [ 12 , 17 , 47 , 49 – 51 ]. Concibido et al [ 52 ] reported that a QTL near the Rhg4 locus could explain 15 % of the total phenotypic variation in PI 209332 to SCN Hg Type 0.…”

Section: Discussionmentioning

confidence: 99%

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

et al. 2015

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BackgroundSoybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most fatal pests of soybean (Glycine max (L.) Merr.) worldwide and causes huge loss of soybean yield each year. Multiple sources of resistance are urgently needed for effective management of SCN via the development of resistant cultivars. The aim of the present study was to investigate the genetic architecture of resistance to SCN HG Type 0 (race 3) and HG Type 1.2.3.5.7 (race 4) in landraces and released elite soybean cultivars mostly from China.ResultsA total of 440 diverse soybean landraces and elite cultivars were screened for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7. Exactly 131 new sources of SCN resistance were identified. Lines were genotyped by SNP markers detected by the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 36,976 SNPs were identified with minor allele frequencies (MAF) > 4 % that were present in 97 % of all the genotypes. Genome-wide association mapping showed that a total of 19 association signals were significantly related to the resistance for the two HG Types. Of the 19 association signals, eight signals overlapped with reported QTL including Rhg1 and Rhg4 genes. Another eight were located in the linked regions encompassing known QTL. Three QTL were found that were not previously reported. The average value of female index (FI) of soybean accessions with resistant alleles was significantly lower than those with susceptible alleles for each peak SNP. Disease resistance proteins with leucine rich regions, cytochrome P450s, protein kinases, zinc finger domain proteins, RING domain proteins, MYB and WRKY transcription activation families were identified. Such proteins may participate in the resistant reaction to SCN and were frequently found in the tightly linked genomic regions of the peak SNPs.ConclusionsGWAS extended understanding of the genetic architecture of SCN resistance in multiple genetic backgrounds. Nineteen association signals were obtained for the resistance to the two Hg Types of SCN. The multiple beneficial alleles from resistant germplasm sources will be useful for the breeding of cultivars with improved resistance to SCN. Analysis of genes near association signals may facilitate the recognition of the causal gene(s) underlying SCN resistances.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1800-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

et al. 2015

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“…The convergence of the Gibbs chains was checked using the test proposed by Heidelberger and Welch (1983) using CODA (convergence diagnosis and output analysis) library in R (Mora and Serra 2014; Arriagada et al 2012). Bayesian point estimation and 95 % credible intervals of population differentiation (F ST ) were calculated using the PROC UNIVARIATE of SAS/STAT Ò (http://www.sas.com).…”

Section: Population Structure and Pcoamentioning

confidence: 99%

Genome-wide association mapping of agronomic traits and carbon isotope discrimination in a worldwide germplasm collection of spring wheat using SNP markers

et al. 2015

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Association mapping has been proposed to identify polymorphisms involved in phenotypic variations and may prove useful in identifying interesting alleles for breeding purposes. Using this approach, a total of 382 cultivars and advanced lines of spring wheat obtained from three breeding programs (Chile, Uruguay and CIMMYT) were evaluated for plant height (PH), kernels per spike (KS), 1,000 kernel weight (TKW), grain yield and carbon isotope discrimination (D 13 C) and tested for genotyping-bysequencing-derived SNP markers across the hexaploid wheat genome. A Bayesian clustering approach via Markov chain Monte Carlo was performed to examine the genetic differentiation (F ST ) among different genetic groups. The results indicated the existence of two distinct and strongly differentiated genetic groups. Cluster I contained 215 genotypes (56.3 %), over 60 % (137/215) of which were collected from CI-MMYT. Cluster II showed the highest F ST value, according to 95 % credible interval. Linkage disequilibrium (LD) among SNPs was calculated for the A, B and D genomes and at the whole-genome level. LD decayed over a longer genetic distance for the D genome than for the A and B genomes. In the A and B genomes, LD declined to 50 % of its initial value at about 2 cM. In the D genome, LD was much more extensive, declining to 50 % of its initial value only at 22 cM. In the whole genome, LD declined to 50 % of its initial value at an average of 4 cM. Important genomic regions associated with complex traits in Electronic supplementary material The online version of this article (spring wheat were identified. Selection on these regions may increase the efficiency of the current breeding programs. Although most of the associations were environment specific, some stable associations were detected for D 13 C, KS, PH and TKW. Chromosomes 1A, 3A, 4A and 5A were the most important chromosomes, as they comprised quantitative trait loci (QTL) for D 13 C, a trait that can be used as an indirect tool for increased water-use efficiency in wheat. Environment-specific genomic regions were detected, indicating the presence of QTL-by-environment interaction. To produce suitable genotypes under contrasting water availability conditions, QTL 9 E interactions (and genotype-by-environment interaction) should be considered in the current spring wheat breeding program.

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“…These procedures determine the marginal posterior distribution of estimates of parameters. The Bayesian approach is considered an important tool in genetic evaluation, since the existing uncertainty about all model parameters (including variance components) is taken into consideration (Arriagada et al 2012, Mora andSerra 2014). In the context of Bayesian inference, all model parameters are considered random variables according to the M Rodovalho et al…”

Section: Introductionmentioning

confidence: 99%

Genetic evaluation of popcorn families using a Bayesian approach via the independence chain algorithm

Rodovalho¹,

Mora

Arriagada

et al. 2014

Crop Breed. Appl. Biotechnol.

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Bayesian mapping of quantitative trait loci (QTL) controlling soybean cyst nematode resistant

Cited by 23 publications

References 65 publications

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

Genome-wide association mapping of agronomic traits and carbon isotope discrimination in a worldwide germplasm collection of spring wheat using SNP markers

Genetic evaluation of popcorn families using a Bayesian approach via the independence chain algorithm

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