Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population
Plant height (PH) and ear height (EH) are two important traits in maize (Zea mays L.), as they are closely related to lodging resistance and planting density. Our objectives were to (1) investigate single-nucleotide polymorphisms (SNPs) that are associated with PH and EH for detecting quantitative t...
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| Format: | Article |
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.963985/full |
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| author | Xingfu Yin Xingfu Yin Yaqi Bi Fuyan Jiang Ruijia Guo Yudong Zhang Jun Fan Manjit S. Kang Xingming Fan |
| author_facet | Xingfu Yin Xingfu Yin Yaqi Bi Fuyan Jiang Ruijia Guo Yudong Zhang Jun Fan Manjit S. Kang Xingming Fan |
| author_sort | Xingfu Yin |
| collection | DOAJ |
| description | Plant height (PH) and ear height (EH) are two important traits in maize (Zea mays L.), as they are closely related to lodging resistance and planting density. Our objectives were to (1) investigate single-nucleotide polymorphisms (SNPs) that are associated with PH and EH for detecting quantitative trait loci (QTL) and new gene that determines PH and EH, (2) explore the value of the QTL in maize breeding, and (3) investigate whether the “triangle heterotic group” theory is applicable for lowering PH and EH to increase yield. Seven inbred female parents were crossed with a common founder male parent Ye 107 to create a nested association mapping (NAM) population. The analysis of phenotypic data on PH and EH revealed wide variation among the parents of the NAM population. Genome-wide association study (GWAS) and high-resolution linkage mapping were conducted using the NAM population, which generated 264,694 SNPs by genotyping-by-sequencing. A total of 105 SNPs and 22 QTL were identified by GWAS and found to be significantly associated with PH and EH. A high-confidence QTL for PH, Qtl-chr1-EP, was identified on chromosome 1 via GWAS and confirmed by linkage analysis in two recombinant inbred line (RIL) populations. Results revealed that the SNP variation in the promoter region of the candidate gene Zm00001d031938, located at Qtl-chr1-EP, which encoded UDP-N-acetylglucosamine-peptide N-acetyl-glucosaminyl-transferase, might decrease PH and EH. Furthermore, the triangle heterotic pattern adopted in maize breeding programs by our team is practicable in selecting high-yield crosses based on the low ratio of EH/PH (EP). |
| first_indexed | 2024-04-12T07:58:38Z |
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| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-12T07:58:38Z |
| publishDate | 2022-08-01 |
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| series | Frontiers in Plant Science |
| spelling | doaj.art-55fdfb1643f7475390b17d6653b4363c2022-12-22T03:41:23ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-08-011310.3389/fpls.2022.963985963985Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping populationXingfu Yin0Xingfu Yin1Yaqi Bi2Fuyan Jiang3Ruijia Guo4Yudong Zhang5Jun Fan6Manjit S. Kang7Xingming Fan8College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaDepartment of Plant Pathology, Kansas State University, Manhattan, KS, United StatesInstitute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, ChinaPlant height (PH) and ear height (EH) are two important traits in maize (Zea mays L.), as they are closely related to lodging resistance and planting density. Our objectives were to (1) investigate single-nucleotide polymorphisms (SNPs) that are associated with PH and EH for detecting quantitative trait loci (QTL) and new gene that determines PH and EH, (2) explore the value of the QTL in maize breeding, and (3) investigate whether the “triangle heterotic group” theory is applicable for lowering PH and EH to increase yield. Seven inbred female parents were crossed with a common founder male parent Ye 107 to create a nested association mapping (NAM) population. The analysis of phenotypic data on PH and EH revealed wide variation among the parents of the NAM population. Genome-wide association study (GWAS) and high-resolution linkage mapping were conducted using the NAM population, which generated 264,694 SNPs by genotyping-by-sequencing. A total of 105 SNPs and 22 QTL were identified by GWAS and found to be significantly associated with PH and EH. A high-confidence QTL for PH, Qtl-chr1-EP, was identified on chromosome 1 via GWAS and confirmed by linkage analysis in two recombinant inbred line (RIL) populations. Results revealed that the SNP variation in the promoter region of the candidate gene Zm00001d031938, located at Qtl-chr1-EP, which encoded UDP-N-acetylglucosamine-peptide N-acetyl-glucosaminyl-transferase, might decrease PH and EH. Furthermore, the triangle heterotic pattern adopted in maize breeding programs by our team is practicable in selecting high-yield crosses based on the low ratio of EH/PH (EP).https://www.frontiersin.org/articles/10.3389/fpls.2022.963985/fullplant heightear heightmaizenested-association mappinggenome-wide association study |
| spellingShingle | Xingfu Yin Xingfu Yin Yaqi Bi Fuyan Jiang Ruijia Guo Yudong Zhang Jun Fan Manjit S. Kang Xingming Fan Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population Frontiers in Plant Science plant height ear height maize nested-association mapping genome-wide association study |
| title | Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population |
| title_full | Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population |
| title_fullStr | Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population |
| title_full_unstemmed | Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population |
| title_short | Fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested-association mapping population |
| title_sort | fine mapping of candidate quantitative trait loci for plant and ear height in a maize nested association mapping population |
| topic | plant height ear height maize nested-association mapping genome-wide association study |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.963985/full |
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