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Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population

The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), fa...

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Autores principales: Wang, Lei, Liu, Fangdong, Hao, Xiaoshuai, Wang, Wubin, Xing, Guangnan, Luo, Jingjing, Zhou, Guodong, He, Jianbo, Gai, Junyi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7947801/
https://www.ncbi.nlm.nih.gov/pubmed/33719333
http://dx.doi.org/10.3389/fgene.2021.600444
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author Wang, Lei
Liu, Fangdong
Hao, Xiaoshuai
Wang, Wubin
Xing, Guangnan
Luo, Jingjing
Zhou, Guodong
He, Jianbo
Gai, Junyi
author_facet Wang, Lei
Liu, Fangdong
Hao, Xiaoshuai
Wang, Wubin
Xing, Guangnan
Luo, Jingjing
Zhou, Guodong
He, Jianbo
Gai, Junyi
author_sort Wang, Lei
collection PubMed
description The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), farmer landraces (LR), and released cultivars (RC). Samples were evaluated in the Photosynthetic System II imaging platform at Nanjing Agricultural University. The NDVI and CHL data were obtained from hyperspectral reflectance images in a randomized incomplete block design experiment with two replicates. The NDVI and CHL ranged from 0.05–0.18 and 1.20–4.78, had averages of 0.11 and 3.57, and had heritabilities of 78.3% and 69.2%, respectively; the values of NDVI and CHL were both significantly higher in LR and RC than in WA. Using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) method, 38 and 32 QTLs with 89 and 82 alleles and 2–4 and 2–6 alleles per locus were identified for NDVI and CHL, respectively, which explained 48.36% and 51.35% of the phenotypic variation for NDVI and CHL, respectively. The QTL-allele matrices were established and separated into WA, LR, and RC submatrices. From WA to LR + RC, 4 alleles and 2 new loci emerged, and 1 allele was excluded for NDVI, whereas 6 alleles emerged, and no alleles were excluded, in LR + RC for CHL. Recombination was the major motivation of evolutionary differences. For NDVI and CHL, 39 and 32 candidate genes were annotated and assigned to GO groups, respectively, indicating a complex gene network. The NDVI and CHL were upstream traits that were relatively conservative in their genetic changes compared with those of downstream agronomic traits. High-throughput phenotyping integrated with RTM-GWAS provides an efficient procedure for studying the population genetics of traits.
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spelling pubmed-79478012021-03-12 Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population Wang, Lei Liu, Fangdong Hao, Xiaoshuai Wang, Wubin Xing, Guangnan Luo, Jingjing Zhou, Guodong He, Jianbo Gai, Junyi Front Genet Genetics The QTL-allele system underlying two spectral reflectance physiological traits, NDVI (normalized difference vegetation index) and CHL (chlorophyll index), related to plant growth and yield was studied in the Chinese soybean germplasm population (CSGP), which consisted of 341 wild accessions (WA), farmer landraces (LR), and released cultivars (RC). Samples were evaluated in the Photosynthetic System II imaging platform at Nanjing Agricultural University. The NDVI and CHL data were obtained from hyperspectral reflectance images in a randomized incomplete block design experiment with two replicates. The NDVI and CHL ranged from 0.05–0.18 and 1.20–4.78, had averages of 0.11 and 3.57, and had heritabilities of 78.3% and 69.2%, respectively; the values of NDVI and CHL were both significantly higher in LR and RC than in WA. Using the RTM-GWAS (restricted two-stage multi-locus genome-wide association study) method, 38 and 32 QTLs with 89 and 82 alleles and 2–4 and 2–6 alleles per locus were identified for NDVI and CHL, respectively, which explained 48.36% and 51.35% of the phenotypic variation for NDVI and CHL, respectively. The QTL-allele matrices were established and separated into WA, LR, and RC submatrices. From WA to LR + RC, 4 alleles and 2 new loci emerged, and 1 allele was excluded for NDVI, whereas 6 alleles emerged, and no alleles were excluded, in LR + RC for CHL. Recombination was the major motivation of evolutionary differences. For NDVI and CHL, 39 and 32 candidate genes were annotated and assigned to GO groups, respectively, indicating a complex gene network. The NDVI and CHL were upstream traits that were relatively conservative in their genetic changes compared with those of downstream agronomic traits. High-throughput phenotyping integrated with RTM-GWAS provides an efficient procedure for studying the population genetics of traits. Frontiers Media S.A. 2021-02-25 /pmc/articles/PMC7947801/ /pubmed/33719333 http://dx.doi.org/10.3389/fgene.2021.600444 Text en Copyright © 2021 Wang, Liu, Hao, Wang, Xing, Luo, Zhou, He and Gai. http://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 Genetics
Wang, Lei
Liu, Fangdong
Hao, Xiaoshuai
Wang, Wubin
Xing, Guangnan
Luo, Jingjing
Zhou, Guodong
He, Jianbo
Gai, Junyi
Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population
title Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population
title_full Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population
title_fullStr Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population
title_full_unstemmed Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population
title_short Identification of the QTL-allele System Underlying Two High-Throughput Physiological Traits in the Chinese Soybean Germplasm Population
title_sort identification of the qtl-allele system underlying two high-throughput physiological traits in the chinese soybean germplasm population
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7947801/
https://www.ncbi.nlm.nih.gov/pubmed/33719333
http://dx.doi.org/10.3389/fgene.2021.600444
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