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Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)

Potatoes are an important source of food for millions of people worldwide. Biotic stresses, notably late blight and potato cyst nematodes (PCN) pose a major threat to potato production worldwide, and knowledge of genes controlling these traits is limited. A genome-wide association mapping study was...

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Autores principales: Sood, Salej, Bhardwaj, Vinay, Bairwa, Aarti, Dalamu, Sharma, Sanjeev, Sharma, Ashwani K., Kumar, Ashwani, Lal, Mehi, Kumar, Vinod
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10582711/
https://www.ncbi.nlm.nih.gov/pubmed/37860256
http://dx.doi.org/10.3389/fpls.2023.1211472
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author Sood, Salej
Bhardwaj, Vinay
Bairwa, Aarti
Dalamu
Sharma, Sanjeev
Sharma, Ashwani K.
Kumar, Ashwani
Lal, Mehi
Kumar, Vinod
author_facet Sood, Salej
Bhardwaj, Vinay
Bairwa, Aarti
Dalamu
Sharma, Sanjeev
Sharma, Ashwani K.
Kumar, Ashwani
Lal, Mehi
Kumar, Vinod
author_sort Sood, Salej
collection PubMed
description Potatoes are an important source of food for millions of people worldwide. Biotic stresses, notably late blight and potato cyst nematodes (PCN) pose a major threat to potato production worldwide, and knowledge of genes controlling these traits is limited. A genome-wide association mapping study was conducted to identify the genomic regulators controlling these biotic stresses, and the genomic prediction accuracy was worked out using the GBLUP model of genomic selection (GS) in a panel of 222 diverse potato accessions. The phenotype data on resistance to late blight and two PCN species (Globodera pallida and G. rostochiensis) were recorded for three and two consecutive years, respectively. The potato panel was genotyped using genotyping by sequencing (GBS), and 1,20,622 SNP markers were identified. A total of 7 SNP associations for late blight resistance, 9 and 11 for G. pallida and G. rostochiensis, respectively, were detected by additive and simplex dominance models of GWAS. The associated SNPs were distributed across the chromosomes, but most of the associations were found on chromosomes 5, 10 and 11, which have been earlier reported as the hotspots of disease-resistance genes. The GS prediction accuracy estimates were low to moderate for resistance to G. pallida (0.04-0.14) and G. rostochiensis (0.14-0.21), while late blight resistance showed a high prediction accuracy of 0.42-0.51. This study provides information on the complex genetic nature of these biotic stress traits in potatoes and putative SNP markers for resistance breeding.
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spelling pubmed-105827112023-10-19 Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.) Sood, Salej Bhardwaj, Vinay Bairwa, Aarti Dalamu Sharma, Sanjeev Sharma, Ashwani K. Kumar, Ashwani Lal, Mehi Kumar, Vinod Front Plant Sci Plant Science Potatoes are an important source of food for millions of people worldwide. Biotic stresses, notably late blight and potato cyst nematodes (PCN) pose a major threat to potato production worldwide, and knowledge of genes controlling these traits is limited. A genome-wide association mapping study was conducted to identify the genomic regulators controlling these biotic stresses, and the genomic prediction accuracy was worked out using the GBLUP model of genomic selection (GS) in a panel of 222 diverse potato accessions. The phenotype data on resistance to late blight and two PCN species (Globodera pallida and G. rostochiensis) were recorded for three and two consecutive years, respectively. The potato panel was genotyped using genotyping by sequencing (GBS), and 1,20,622 SNP markers were identified. A total of 7 SNP associations for late blight resistance, 9 and 11 for G. pallida and G. rostochiensis, respectively, were detected by additive and simplex dominance models of GWAS. The associated SNPs were distributed across the chromosomes, but most of the associations were found on chromosomes 5, 10 and 11, which have been earlier reported as the hotspots of disease-resistance genes. The GS prediction accuracy estimates were low to moderate for resistance to G. pallida (0.04-0.14) and G. rostochiensis (0.14-0.21), while late blight resistance showed a high prediction accuracy of 0.42-0.51. This study provides information on the complex genetic nature of these biotic stress traits in potatoes and putative SNP markers for resistance breeding. Frontiers Media S.A. 2023-10-04 /pmc/articles/PMC10582711/ /pubmed/37860256 http://dx.doi.org/10.3389/fpls.2023.1211472 Text en Copyright © 2023 Sood, Bhardwaj, Bairwa, Dalamu, Sharma, Sharma, Kumar, Lal and Kumar https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Sood, Salej
Bhardwaj, Vinay
Bairwa, Aarti
Dalamu
Sharma, Sanjeev
Sharma, Ashwani K.
Kumar, Ashwani
Lal, Mehi
Kumar, Vinod
Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)
title Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)
title_full Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)
title_fullStr Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)
title_full_unstemmed Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)
title_short Genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (Solanum tuberosum L.)
title_sort genome-wide association mapping and genomic prediction for late blight and potato cyst nematode resistance in potato (solanum tuberosum l.)
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10582711/
https://www.ncbi.nlm.nih.gov/pubmed/37860256
http://dx.doi.org/10.3389/fpls.2023.1211472
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