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Kim Y, Choi MG, Lee MH, Cho C, Choi JY, Kim SJ, Kang CS, Park CS, Jang KC, Mo Y, Choi C. Genome-wide association study to identify the genomic loci associated with wheat heading date variation under autumn-sowing conditions. PLoS One 2025; 20:e0322306. [PMID: 40305553 PMCID: PMC12043121 DOI: 10.1371/journal.pone.0322306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Accepted: 03/19/2025] [Indexed: 05/02/2025] Open
Abstract
The present study aimed to identify genetic loci associated with days to heading (DTH) in wheat under autumn-sowing conditions in Korea, where early heading is critical owing to the overlap between the wheat harvest and the rainy season. We evaluated 530 wheat core collections over five years, focusing on known heading date genes VRN-1 and PPD-1, and conducted a genome-wide association study (GWAS) to identify new genetic loci related to DTH. The results revealed that Korean accessions exhibited the earliest DTH, with modern Korean varieties heading even earlier, reflecting a strong breeding focus on early heading. Among the existing heading date genes, VRN-1 and PPD-D1 were significantly associated with DTH in the wheat core collection. However, all Korean varieties carried the same alleles for each of VRN-A1, PPD-A1, and PPD-D1, resulting in low genetic diversity, which rendered the existing heading date genes insufficient to fully account for the variation in DTH within the Korean varieties. GWAS identified nine single nucleotide polymorphisms (SNPs) associated with DTH in Group A (entire collection filtered, n=518) and six in Group B (accessions with genotypes identical to Korean varieties filtered, n=231). Four key SNPs (AX-95222044 and AX-94685526 in Group A, and AX-94550996 and AX-94970315 in Group B) were selected based on their effect sizes on DTH. In both groups, accessions with alleles for early heading at both of the selected SNPs exhibited the earliest DTH, advancing by 7.7 to 8.9 days. These findings suggest that the selected SNPs, particularly those reflecting the genotypes of Korean varieties, effectively explain the variations in DTH among Korean varieties and could enhance wheat breeding efficiency in Korea. Further research is needed to validate the four selected SNPs and identify the underlying genes, which could serve as valuable markers for developing early-heading wheat varieties suited to Korean autumn-sowing conditions.
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Affiliation(s)
- Yurim Kim
- National Institute of Crop Science, Wanju, Republic of Korea
| | - Myoung-Goo Choi
- National Institute of Crop Science, Wanju, Republic of Korea
| | - Myoung Hui Lee
- National Institute of Crop Science, Wanju, Republic of Korea
| | - Chuloh Cho
- National Institute of Crop Science, Wanju, Republic of Korea
| | - Jun Yong Choi
- Department of Central Area Crop Science, National Institute of Crop Science, Suwon, Republic of Korea
| | - Suk-Jin Kim
- National Institute of Crop Science, Wanju, Republic of Korea
| | - Chon-Sik Kang
- National Institute of Crop Science, Wanju, Republic of Korea
| | - Chul Soo Park
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Ki-Chang Jang
- National Institute of Crop Science, Wanju, Republic of Korea
| | - Youngjun Mo
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Changhyun Choi
- National Institute of Crop Science, Wanju, Republic of Korea
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Fourquet L, Barber T, Campos-Mantello C, Howell P, Orman-Ligeza B, Percival-Alwyn L, Rose GA, Sheehan H, Wright TIC, Longin F, Würschum T, Novoselovic D, Greenland AJ, Mackay IJ, Cockram J, Bentley AR. An eight-founder wheat MAGIC population allows fine-mapping of flowering time loci and provides novel insights into the genetic control of flowering time. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:277. [PMID: 39576319 PMCID: PMC11584503 DOI: 10.1007/s00122-024-04787-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 11/11/2024] [Indexed: 11/24/2024]
Abstract
Flowering time synchronizes reproductive development with favorable environmental conditions to optimize yield. Improved understanding of the genetic control of flowering will help optimize varietal adaptation to future agricultural systems under climate change. Here, we investigate the genetic basis of flowering time in winter wheat (Triticum aestivum L.) using an eight-founder multi-parent advanced generation intercross (MAGIC) population. Flowering time data was collected from field trials across six growing seasons in the United Kingdom, followed by genetic analysis using a combination of linear modelling, simple interval mapping and composite interval mapping, using either single markers or founder haplotype probabilities. We detected 57 quantitative trait loci (QTL) across three growth stages linked to flowering time, of which 17 QTL were identified only when the major photoperiod response locus Ppd-D1 was included as a covariate. Of the 57 loci, ten were identified using all genetic mapping approaches and classified as 'major' QTL, including homoeologous loci on chromosomes 1B and 1D, and 4A and 4B. Additional Earliness per se flowering time QTL were identified, along with growth stage- and year-specific effects. Furthermore, six of the main-effect QTL were found to interact epistatically with Ppd-D1. Finally, we exploited residual heterozygosity in the MAGIC recombinant inbred lines to Mendelize the Earliness per se QTL QFt.niab-5A.03, which was confirmed to modulate flowering time by at least four days. This work provides detailed understanding of the genetic control of phenological variation within varieties relevant to the north-western European wheat genepool, aiding informed manipulation of flowering time in wheat breeding.
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Affiliation(s)
| | - Tobias Barber
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Phil Howell
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | | | - Gemma A Rose
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | | | - Friedrich Longin
- State Plant Breeding Institute, University of Hohenheim, Hohenheim, Germany
| | - Tobias Würschum
- State Plant Breeding Institute, University of Hohenheim, Hohenheim, Germany
| | | | | | - Ian J Mackay
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Scotland's Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh, EH9 3JG, UK
| | - James Cockram
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
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Burridge AJ, Winfield M, Przewieslik‐Allen A, Edwards KJ, Siddique I, Barral‐Arca R, Griffiths S, Cheng S, Huang Z, Feng C, Dreisigacker S, Bentley AR, Brown‐Guedira G, Barker GL. Development of a next generation SNP genotyping array for wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2235-2247. [PMID: 38520342 PMCID: PMC11258986 DOI: 10.1111/pbi.14341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024]
Abstract
High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the 'Triticum aestivum Next Generation' array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins 'Core Collection'. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.
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Affiliation(s)
| | - Mark Winfield
- School of Biological SciencesUniversity of BristolBristolUK
| | | | | | - Imteaz Siddique
- Thermo Fisher Scientific3450 Central ExpresswaySanta ClaraCAUSA
| | | | | | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Zejian Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Cong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | | | | | - Gina Brown‐Guedira
- Plant Science Research UnitUSDA Agricultural Research ServiceRaleighNCUSA
| | - Gary L. Barker
- School of Biological SciencesUniversity of BristolBristolUK
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