GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola

Prom, Louis K.; Ahn, Ezekiel; Isakeit, Thomas; Magill, Clint

doi:10.1007/s00122-019-03285-5

Cited by 33 publications

(45 citation statements)

References 49 publications

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“…A total of 55 accessions (22%) with disease incidence scores ≤2.0 across experiments were classified as resistant (Additional file 1: Table S3). Previous studies showed most of the accessions classified as resistant in Puerto Rico were resistant at Georgia and Texas, USA [17,29]. Thus, further screening at other locations could be limited to these 55 resistant accessions.…”

Section: Anthracnose Resistance Responsementioning

confidence: 99%

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

Cuevas

Prom

2020

BMC Genomics

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Background: The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response. Results: We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima's D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions. Conclusions: The NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.

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Section: Anthracnose Resistance Responsementioning

confidence: 99%

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

Cuevas

Prom

2020

BMC Genomics

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“…Genome-wide association analysis within the anthracnose resistance locus Three previous GWAS analyses for anthracnose resistance response in the sorghum association panel (SAP) (Cuevas et al 2018;Prom et al 2019), and NPGS Ethiopian collection (Cuevas et al 2019) were combined to conduct an association analysis limited to the 276 SNPs present in the resistance locus on chromosome 5 (65.17 to 65.64 Mb). A total of 280 accessions from SAP have been evaluated against pathotypes from Puerto Rico, Georgia and Texas, U.S.A. of which 35 accessions were found to be resistant across locations.…”

Section: Fine-mapping Of Anthracnose Resistance Locusmentioning

confidence: 99%

“…The sorghum association panel (SAP) is comprised of 149 U.S. breeding lines and 228 lines adapted to temperate regions and was assembled to capture the majority of genetic diversity present in sorghum germplasm and breeding programs (Casa et al 2008). Among 335 accessions from the SAP evaluated against pathotypes from Puerto Rico, Texas and Georgia, 37 were resistant to all tested pathotypes of anthracnose (Cuevas et al 2018;Prom et al 2019). Unfortunately, the lack of information on the genetic control of resistance in these sources has limited their use in breeding programs.…”

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confidence: 99%

Genomic Dissection of Anthracnose (Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14

Cruet-Burgos

Cuevas

Prom

et al. 2020

G3 Genes|Genomes|Genetics

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Sorghum production is expanding to warmer and more humid regions where its production is being limited by multiple fungal pathogens. Anthracnose, caused by Colletotrichum sublineolum, is one of the major diseases in these regions, where it can cause yield losses of both grain and biomass. In this study, 114 recombinant inbred lines (RILs) derived from resistant sorghum line SC112-14 were evaluated at four distinct geographic locations in the United States for response to anthracnose. A genome scan using a high-density linkage map of 3,838 single nucleotide polymorphisms (SNPs) detected two loci at 5.25 and 1.18 Mb on chromosomes 5 and 6, respectively, that explain up to 59% and 44% of the observed phenotypic variation. A bin-mapping approach using a subset of 31 highly informative RILs was employed to determine the disease response to inoculation with ten anthracnose pathotypes in the greenhouse. A genome scan showed that the 5.25 Mb region on chromosome 5 is associated with a resistance response to nine pathotypes. Five SNP markers were developed and used to fine map the locus on chromosome 5 by evaluating 1,500 segregating F2:3 progenies. Based on the genotypic and phenotypic analyses of 11 recombinants, the locus was narrowed down to a 470-kb genomic region. Following a genome-wide association study based on 574 accessions previously phenotyped and genotyped, the resistance locus was delimited to a 34-kb genomic interval with five candidate genes. All five candidate genes encode proteins associated with plant immune systems, suggesting they may act in synergy in the resistance response.

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“…Recently, GWAS of minor cereals have focused on practical traits, whereas earlier studies tended to focus on the evaluation and potential of using GWAS in each target species. Disease resistance is one of the most commonly targeted traits for GWAS of oat (Montilla-Bascón et al 2015), emmer wheat (Liu et al 2017), and sorghum (Prom et al 2019). To utilize the rich nutrients of minor cereals (e.g., reviewed by Muthamilarasan et al (2016)), several GWAS results for grain ingredients have been reported in sorghum (Rhodes et al 2014), oat (Newell et al 2012), and foxtail millet (Jaiswal et al 2019).…”

Section: Genome-wide Association Studiesmentioning

confidence: 99%

Genomics-assisted breeding in minor and pseudo-cereals

Yabe

Iwata

2020

Breed. Sci.

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Minor and pseudo-cereals, which can grow with lower input and often produce specific nutrients compared to major cereal crops, are attracting worldwide attention. Since these crops generally have a large genetic diversity in a breeding population, rapid genetic improvement can be possible by the application of genomicsassisted breeding methods. In this review, we discuss studies related to biparental quantitative trait locus (QTL) mapping, genome-wide association study, and genomic selection for minor and pseudo-cereals. Especially, we focus on the current progress in a pseudo-cereal, buckwheat. Prospects for the practical utilization of genomics-assisted breeding in minor and pseudo-cereals are discussed including the issues to overcome especially for these crops.

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GWAS analysis of sorghum association panel lines identifies SNPs associated with disease response to Texas isolates of Colletotrichum sublineola

Cited by 33 publications

References 49 publications

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

Genomic Dissection of Anthracnose (Colletotrichum sublineolum) Resistance Response in Sorghum Differential Line SC112-14

Genomics-assisted breeding in minor and pseudo-cereals

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