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Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet

Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha(−1)) and stagnant in the major production regions, including Burkina Faso. The lo...

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Autores principales: Rouamba, Armel, Shimelis, Hussein, Drabo, Inoussa, Mrema, Emmanuel, Ojiewo, Christopher Ochieng, Mwadzingeni, Learnmore, Rathore, Abhishek
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10567810/
https://www.ncbi.nlm.nih.gov/pubmed/37821558
http://dx.doi.org/10.1038/s41598-023-44046-1
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author Rouamba, Armel
Shimelis, Hussein
Drabo, Inoussa
Mrema, Emmanuel
Ojiewo, Christopher Ochieng
Mwadzingeni, Learnmore
Rathore, Abhishek
author_facet Rouamba, Armel
Shimelis, Hussein
Drabo, Inoussa
Mrema, Emmanuel
Ojiewo, Christopher Ochieng
Mwadzingeni, Learnmore
Rathore, Abhishek
author_sort Rouamba, Armel
collection PubMed
description Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha(−1)) and stagnant in the major production regions, including Burkina Faso. The low productivity of pearl millet is mainly attributable to a lack of improved varieties, Striga hermonthica [Sh] infestation, downy mildew infection, and recurrent heat and drought stress. Developing high-yielding and Striga-resistant pearl millet varieties that satisfy the farmers’ and market needs requires the identification of yield-promoting genes linked to economic traits to facilitate marker-assisted selection and gene pyramiding. The objective of this study was to undertake genome-wide association analyses of agronomic traits and Sh resistance among 150 pearl millet genotypes to identify genetic markers for marker-assisted breeding and trait introgression. The pearl millet genotypes were phenotyped in Sh hotspot fields and screen house conditions. Twenty-nine million single nucleotide polymorphisms (SNPs) initially generated from 345 pearl millet genotypes were filtered, and 256 K SNPs were selected and used in the present study. Phenotypic data were collected on days to flowering, plant height, number of tillers, panicle length, panicle weight, thousand-grain weight, grain weight, number of emerged Striga and area under the Striga number progress curve (ASNPC). Agronomic and Sh parameters were subjected to combined analysis of variance, while genome-wide association analysis was performed on phenotypic and SNPs data. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for Sh parameters and agronomic traits. Further, there were significant genotype by Sh interaction for the number of Sh and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged Sh located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs were associated with days-to-50%-flowering on chromosomes 3, 5, 6, and 7, while five were associated with panicle length on chromosomes 2, 3, and 4. Seven SNPs were linked to thousand-grain weight on chromosomes 2, 3, and 6. The putative SNP markers associated with a low number of emerged Sh and agronomic traits in the assessed genotypes are valuable genomic resources for accelerated breeding and variety deployment of pearl millet with Sh resistance and farmer- and market-preferred agronomic traits.
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spelling pubmed-105678102023-10-13 Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet Rouamba, Armel Shimelis, Hussein Drabo, Inoussa Mrema, Emmanuel Ojiewo, Christopher Ochieng Mwadzingeni, Learnmore Rathore, Abhishek Sci Rep Article Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha(−1)) and stagnant in the major production regions, including Burkina Faso. The low productivity of pearl millet is mainly attributable to a lack of improved varieties, Striga hermonthica [Sh] infestation, downy mildew infection, and recurrent heat and drought stress. Developing high-yielding and Striga-resistant pearl millet varieties that satisfy the farmers’ and market needs requires the identification of yield-promoting genes linked to economic traits to facilitate marker-assisted selection and gene pyramiding. The objective of this study was to undertake genome-wide association analyses of agronomic traits and Sh resistance among 150 pearl millet genotypes to identify genetic markers for marker-assisted breeding and trait introgression. The pearl millet genotypes were phenotyped in Sh hotspot fields and screen house conditions. Twenty-nine million single nucleotide polymorphisms (SNPs) initially generated from 345 pearl millet genotypes were filtered, and 256 K SNPs were selected and used in the present study. Phenotypic data were collected on days to flowering, plant height, number of tillers, panicle length, panicle weight, thousand-grain weight, grain weight, number of emerged Striga and area under the Striga number progress curve (ASNPC). Agronomic and Sh parameters were subjected to combined analysis of variance, while genome-wide association analysis was performed on phenotypic and SNPs data. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for Sh parameters and agronomic traits. Further, there were significant genotype by Sh interaction for the number of Sh and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged Sh located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs were associated with days-to-50%-flowering on chromosomes 3, 5, 6, and 7, while five were associated with panicle length on chromosomes 2, 3, and 4. Seven SNPs were linked to thousand-grain weight on chromosomes 2, 3, and 6. The putative SNP markers associated with a low number of emerged Sh and agronomic traits in the assessed genotypes are valuable genomic resources for accelerated breeding and variety deployment of pearl millet with Sh resistance and farmer- and market-preferred agronomic traits. Nature Publishing Group UK 2023-10-11 /pmc/articles/PMC10567810/ /pubmed/37821558 http://dx.doi.org/10.1038/s41598-023-44046-1 Text en © The Author(s) 2023, corrected publication 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Rouamba, Armel
Shimelis, Hussein
Drabo, Inoussa
Mrema, Emmanuel
Ojiewo, Christopher Ochieng
Mwadzingeni, Learnmore
Rathore, Abhishek
Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet
title Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet
title_full Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet
title_fullStr Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet
title_full_unstemmed Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet
title_short Genome-wide association analyses of agronomic traits and Striga hermonthica resistance in pearl millet
title_sort genome-wide association analyses of agronomic traits and striga hermonthica resistance in pearl millet
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10567810/
https://www.ncbi.nlm.nih.gov/pubmed/37821558
http://dx.doi.org/10.1038/s41598-023-44046-1
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