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Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations

Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were scr...

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Autores principales: Feng, Fangjun, Ma, Xiaosong, Yan, Ming, Zhang, Hong, Mei, Daoliang, Fan, Peiqing, Xu, Xiaoyan, Wei, Chunlong, Lou, Qiaojun, Li, Tianfei, Liu, Hongyan, Luo, Lijun, Mei, Hanwei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10385686/
https://www.ncbi.nlm.nih.gov/pubmed/37514357
http://dx.doi.org/10.3390/plants12142743
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author Feng, Fangjun
Ma, Xiaosong
Yan, Ming
Zhang, Hong
Mei, Daoliang
Fan, Peiqing
Xu, Xiaoyan
Wei, Chunlong
Lou, Qiaojun
Li, Tianfei
Liu, Hongyan
Luo, Lijun
Mei, Hanwei
author_facet Feng, Fangjun
Ma, Xiaosong
Yan, Ming
Zhang, Hong
Mei, Daoliang
Fan, Peiqing
Xu, Xiaoyan
Wei, Chunlong
Lou, Qiaojun
Li, Tianfei
Liu, Hongyan
Luo, Lijun
Mei, Hanwei
author_sort Feng, Fangjun
collection PubMed
description Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by −log(10)(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.
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spelling pubmed-103856862023-07-30 Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations Feng, Fangjun Ma, Xiaosong Yan, Ming Zhang, Hong Mei, Daoliang Fan, Peiqing Xu, Xiaoyan Wei, Chunlong Lou, Qiaojun Li, Tianfei Liu, Hongyan Luo, Lijun Mei, Hanwei Plants (Basel) Article Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by −log(10)(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed. MDPI 2023-07-24 /pmc/articles/PMC10385686/ /pubmed/37514357 http://dx.doi.org/10.3390/plants12142743 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Feng, Fangjun
Ma, Xiaosong
Yan, Ming
Zhang, Hong
Mei, Daoliang
Fan, Peiqing
Xu, Xiaoyan
Wei, Chunlong
Lou, Qiaojun
Li, Tianfei
Liu, Hongyan
Luo, Lijun
Mei, Hanwei
Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations
title Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations
title_full Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations
title_fullStr Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations
title_full_unstemmed Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations
title_short Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations
title_sort identification of genetic loci for rice seedling mesocotyl elongation in both natural and artificial segregating populations
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10385686/
https://www.ncbi.nlm.nih.gov/pubmed/37514357
http://dx.doi.org/10.3390/plants12142743
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