Genome-Wide Association Analysis for Candidate Genes Contributing to Kernel-Related Traits in Maize

Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel len...

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Published inFrontiers in plant science Vol. 13; p. 872292
Main Authors Qu, Zhibo, Wu, Ying, Hu, Die, Li, Ting, Liang, Hangyu, Ye, Fan, Xue, Jiquan, Xu, Shutu
Format Journal Article
LanguageEnglish
Published Switzerland Frontiers Media S.A 24.05.2022
Subjects
differential expression
expression profile
genome-wide association study
kernel-related traits
maize
Plant Science
differential expression
kernel-related traits
maize
expression profile
genome-wide association study
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Abstract Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel length, kernel width, kernel thickness, and hundred-kernel weight from multiple locations in AM122 and AM180, respectively. Then, genome-wide association mapping was performed based on the maize 6H90K SNP chip. A total of 139 loci were identified as associated with the four traits with < 1 × 10 using two models (FarmCPU and MLM). The transcriptome data showed that 15 of them were expressed differentially in two maize-inbred lines KB182 (small kernel) and KB020 (big kernel) during kernel development. These candidate genes were enriched in regulating peroxidase activity, oxidoreductase, and leaf senescence. The molecular function was major in binding and catalytic activity. This study provided important reference information for exploring maize kernel development mechanisms and applying molecular markers in high-yield breeding.
AbstractList Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel length, kernel width, kernel thickness, and hundred-kernel weight from multiple locations in AM122 and AM180, respectively. Then, genome-wide association mapping was performed based on the maize 6H90K SNP chip. A total of 139 loci were identified as associated with the four traits with p < 1 × 10−4 using two models (FarmCPU and MLM). The transcriptome data showed that 15 of them were expressed differentially in two maize-inbred lines KB182 (small kernel) and KB020 (big kernel) during kernel development. These candidate genes were enriched in regulating peroxidase activity, oxidoreductase, and leaf senescence. The molecular function was major in binding and catalytic activity. This study provided important reference information for exploring maize kernel development mechanisms and applying molecular markers in high-yield breeding.
Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel length, kernel width, kernel thickness, and hundred-kernel weight from multiple locations in AM122 and AM180, respectively. Then, genome-wide association mapping was performed based on the maize 6H90K SNP chip. A total of 139 loci were identified as associated with the four traits with p < 1 × 10 −4 using two models (FarmCPU and MLM). The transcriptome data showed that 15 of them were expressed differentially in two maize-inbred lines KB182 (small kernel) and KB020 (big kernel) during kernel development. These candidate genes were enriched in regulating peroxidase activity, oxidoreductase, and leaf senescence. The molecular function was major in binding and catalytic activity. This study provided important reference information for exploring maize kernel development mechanisms and applying molecular markers in high-yield breeding.
Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize seed development and yield formation. In this study, two associated populations were used for genome-wide association analysis of kernel length, kernel width, kernel thickness, and hundred-kernel weight from multiple locations in AM122 and AM180, respectively. Then, genome-wide association mapping was performed based on the maize 6H90K SNP chip. A total of 139 loci were identified as associated with the four traits with < 1 × 10 using two models (FarmCPU and MLM). The transcriptome data showed that 15 of them were expressed differentially in two maize-inbred lines KB182 (small kernel) and KB020 (big kernel) during kernel development. These candidate genes were enriched in regulating peroxidase activity, oxidoreductase, and leaf senescence. The molecular function was major in binding and catalytic activity. This study provided important reference information for exploring maize kernel development mechanisms and applying molecular markers in high-yield breeding.
Author Xue, Jiquan
Qu, Zhibo
Li, Ting
Wu, Ying
Liang, Hangyu
Hu, Die
Ye, Fan
Xu, Shutu
AuthorAffiliation 2 Maize Engineering Technology Research Centre , Yangling , China
1 Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University , Yangling , China
AuthorAffiliation_xml – name: 1 Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs, College of Agronomy, Northwest A&F University , Yangling , China
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Keywords differential expression
kernel-related traits
maize
expression profile
genome-wide association study
Language English
License Copyright © 2022 Qu, Wu, Hu, Li, Liang, Ye, Xue and Xu.
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Reviewed by: Dawei Xin, Northeast Agricultural University, China; Donghai Mao, Institute of Subtropical Agriculture (CAS), China
Edited by: Guoyou Ye, International Rice Research Institute (IRRI), Philippines
This article was submitted to Plant Breeding, a section of the journal Frontiers in Plant Science
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Snippet Maize grain size is the main factor determining grain yield. Dissecting the genetic basis of maize grain size may help reveal the regulatory mechanism of maize...
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SubjectTerms differential expression
expression profile
genome-wide association study
kernel-related traits
maize
Plant Science
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Title Genome-Wide Association Analysis for Candidate Genes Contributing to Kernel-Related Traits in Maize
URI https://www.ncbi.nlm.nih.gov/pubmed/35685022
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Volume 13
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