Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize
Abstract Background Maize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour...
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| Format: | Article |
| Language: | English |
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BMC
2024-01-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-023-04662-5 |
| _version_ | 1797363504458498048 |
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| author | Weiwei Chen Fangqing Cui Hang Zhu Xiangbo Zhang Siqi Lu Chuanli Lu Hailong Chang Lina Fan Huanzhang Lin Junteng Fang Yuxing An Xuhui Li Yongwen Qi |
| author_facet | Weiwei Chen Fangqing Cui Hang Zhu Xiangbo Zhang Siqi Lu Chuanli Lu Hailong Chang Lina Fan Huanzhang Lin Junteng Fang Yuxing An Xuhui Li Yongwen Qi |
| author_sort | Weiwei Chen |
| collection | DOAJ |
| description | Abstract Background Maize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour traits, an association panel including 244 superior maize inbred lines was used to measure and analyse the six traits related to kernel colour in two environments and was then combined with the about 3 million SNPs covering the whole maize genome in this study. Two models (Q + K, PCA + K) were used for genome-wide association analysis (GWAS) of kernel colour traits. Results We identified 1029QTLs, and two SNPs contained in those QTLs were located in coding regions of Y1 and R1 respectively, two known genes that regulate kernel colour. Fourteen QTLs which contain 19 SNPs were within 200 kb interval of the genes involved in the regulation of kernel colour. 13 high-confidence SNPs repeatedly detected for specific traits, and AA genotypes of rs1_40605594 and rs5_2392770 were the most popular alleles appeared in inbred lines with higher levels. By searching the confident interval of the 13 high-confidence SNPs, a total of 95 candidate genes were identified. Conclusions The genetic loci and candidate genes of maize kernel colour provided in this study will be useful for uncovering the genetic mechanism of maize kernel colour, gene cloning in the future. Furthermore, the identified elite alleles can be used to molecular marker-assisted selection of kernel colour traits. |
| first_indexed | 2024-03-08T16:21:24Z |
| format | Article |
| id | doaj.art-569ccc5503a6427389459b5bb20bbcce |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-03-08T16:21:24Z |
| publishDate | 2024-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-569ccc5503a6427389459b5bb20bbcce2024-01-07T12:18:49ZengBMCBMC Plant Biology1471-22292024-01-0124111110.1186/s12870-023-04662-5Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maizeWeiwei Chen0Fangqing Cui1Hang Zhu2Xiangbo Zhang3Siqi Lu4Chuanli Lu5Hailong Chang6Lina Fan7Huanzhang Lin8Junteng Fang9Yuxing An10Xuhui Li11Yongwen Qi12Institute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceInstitute of Nanfan & Seed Industry, Guangdong Academy of ScienceAbstract Background Maize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour traits, an association panel including 244 superior maize inbred lines was used to measure and analyse the six traits related to kernel colour in two environments and was then combined with the about 3 million SNPs covering the whole maize genome in this study. Two models (Q + K, PCA + K) were used for genome-wide association analysis (GWAS) of kernel colour traits. Results We identified 1029QTLs, and two SNPs contained in those QTLs were located in coding regions of Y1 and R1 respectively, two known genes that regulate kernel colour. Fourteen QTLs which contain 19 SNPs were within 200 kb interval of the genes involved in the regulation of kernel colour. 13 high-confidence SNPs repeatedly detected for specific traits, and AA genotypes of rs1_40605594 and rs5_2392770 were the most popular alleles appeared in inbred lines with higher levels. By searching the confident interval of the 13 high-confidence SNPs, a total of 95 candidate genes were identified. Conclusions The genetic loci and candidate genes of maize kernel colour provided in this study will be useful for uncovering the genetic mechanism of maize kernel colour, gene cloning in the future. Furthermore, the identified elite alleles can be used to molecular marker-assisted selection of kernel colour traits.https://doi.org/10.1186/s12870-023-04662-5MaizeKernel colourGenome-wide association studyCandidate geneElite allele |
| spellingShingle | Weiwei Chen Fangqing Cui Hang Zhu Xiangbo Zhang Siqi Lu Chuanli Lu Hailong Chang Lina Fan Huanzhang Lin Junteng Fang Yuxing An Xuhui Li Yongwen Qi Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize BMC Plant Biology Maize Kernel colour Genome-wide association study Candidate gene Elite allele |
| title | Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize |
| title_full | Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize |
| title_fullStr | Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize |
| title_full_unstemmed | Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize |
| title_short | Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize |
| title_sort | genome wide association study of kernel colour traits and mining of elite alleles from the major loci in maize |
| topic | Maize Kernel colour Genome-wide association study Candidate gene Elite allele |
| url | https://doi.org/10.1186/s12870-023-04662-5 |
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