|
1
|
Li Z, Li X, Liu S, Mai S, Qin Y, Wang S, Zhou Z, Yang K, Huang X, Deng Y, Luo Q, Ren T. Identification and validation of quantitative trait loci for seven quality-related traits in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2025; 138:57. [PMID: 40009158 DOI: 10.1007/s00122-025-04851-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 02/07/2025] [Indexed: 02/27/2025]
Abstract
KEY MESSAGE QTLs for seven different quality traits were mapped. Six QTLs were considered stable and major QTLs, and the genetic effects of the QTLs were validated. Wheat grain quality traits are the key factors for economic value and are largely influenced by genetics and the environment. In this study, a genetic linkage map consisting of 8329 markers spanning 4131.54 cM was constructed using the Wheat55K SNP Array by genotyping a recombinant inbred line population of 304 lines. The quantitative trait loci (QTLs) for the swelling index of glutenin, SDS sedimentation volume (SDSS), wet gluten content, grain protein content, gluten index, grain starch content, and falling number were mapped for multiple years of experiments using the ICIM-BIP, ICIM-MET, and ICIM-EPI methods, respectively. A total of 92 QTLs, 194 cQTLs, and 117 pairs of eQTLs were mapped. Six QTLs, which were QGPC.sau-4A.1, QWGC.sau-4A, QSDSS.sau-1A.1, QGI.sau-1A, QFN.sau-4D, and QSIG.sau-1A, were considered major and stable QTLs. BLAST results showed that except QFN.sau-4D, the other 5 QTLs were new. Eight QTL clusters that contained 19 QTLs were also detected, and all the major and stable QTLs were located in these QTL clusters. Kompetitive allele-specific PCR markers closely linked to the six QTLs were designed. The genetic effects of the major and stable QTLs were successfully confirmed in different populations. These results provide new resources for breeding of high-quality wheat in the future.
Collapse
Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xinli Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Sunhong Liu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shijun Mai
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yitian Qin
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shiyu Wang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Zijie Zhou
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Kehan Yang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xinyu Huang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yawen Deng
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Qinyi Luo
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Tianheng Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China.
| |
Collapse
|
|
2
|
Wang D, Xie J, Wang J, Mu M, Xiong H, Ma F, Li P, Jia M, Li S, Li J, Zhu M, Li P, Guan H, Zhang Y, Li H. Unraveling Allelic Impacts on Pre-Harvest Sprouting Resistance in TaVP1-B of Chinese Wheat Accessions Using Pan-Genome. PLANTS (BASEL, SWITZERLAND) 2025; 14:504. [PMID: 40006763 PMCID: PMC11859669 DOI: 10.3390/plants14040504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2024] [Revised: 02/04/2025] [Accepted: 02/05/2025] [Indexed: 02/27/2025]
Abstract
The TaVP1-B gene, located on the 3B chromosome of wheat, is a homolog of the Viviparous-1 (VP-1) gene of maize and was reported to confer resistance to pre-harvest sprouting (PHS) in wheat. In this study, the structure of the TaVP1-B gene was analyzed using the wheat pan-genome consisting of 20 released cultivars (19 wheat are from China), and 3 single nucleotide polymorphisms (SNPs), which were identified at the 496 bp, 524 bp, and 1548 bp of the TaVP1-B CDS region, respectively. Haplotypes analysis showed that these SNPs were in complete linkage disequilibrium and that only two haplotypes designated as hap1 (TGG) and hap2 (GAA) were present. Association analysis between TaVP1-B haplotypes and PHS resistance of the 20 wheat cultivars in four experiment environments revealed that the average PHS resistance of accessions with hap1 was significantly better than that of accessions with hap2, which infers the effects of TaVP1-B on wheat PHS resistance. To further investigate the impacts of alleles at the TaVP1-B locus on PHS resistance, the SNP at 1548 bp of the TaVP1-B CDS region was converted to a KASP marker, which was used for genotyping 304 Chinese wheat cultivars, whose PHS resistance was evaluated in three environments. The average sprouting rates (SRs) of 135 wheat cultivars with the hap1 were significantly lower than the 169 cultivars with the hap2, validating the impacts of TaVP1-B on PHS resistance in Chinese wheat. The present study provided the breeding-friendly marker for functional variants in the TaVP1-B gene, which can be used for genetic improvement of PHS resistance in wheat.
Collapse
Affiliation(s)
- Danfeng Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University/Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou 466001, China; (D.W.); (J.W.); (M.M.)
- Henan International Joint Laboratory of Translational Biology, Zhoukou 466001, China;
| | - Jinjin Xie
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng 475000, China;
| | - Jingwen Wang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University/Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou 466001, China; (D.W.); (J.W.); (M.M.)
- Henan Plant Gene and Molecular Breeding Engineering Research Center, Zhoukou 466001, China;
| | - Mengdi Mu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University/Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou 466001, China; (D.W.); (J.W.); (M.M.)
- Henan Plant Gene and Molecular Breeding Engineering Research Center, Zhoukou 466001, China;
| | - Haifeng Xiong
- Henan Plant Gene and Molecular Breeding Engineering Research Center, Zhoukou 466001, China;
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
| | - Fengshuo Ma
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
- Henan Crop Molecular Design Breeding and Cultivation Engineering Technology Research Center, Zhoukou 466001, China
| | - Peizhen Li
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
- Henan Crop Molecular Design Breeding and Cultivation Engineering Technology Research Center, Zhoukou 466001, China
| | - Menghan Jia
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
- Henan Crop Molecular Design Breeding and Cultivation Engineering Technology Research Center, Zhoukou 466001, China
| | - Shuangjing Li
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
- Henan Crop Molecular Design Breeding and Cultivation Engineering Technology Research Center, Zhoukou 466001, China
| | - Jiaxin Li
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
- Henan Crop Molecular Design Breeding and Cultivation Engineering Technology Research Center, Zhoukou 466001, China
| | - Mingyue Zhu
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
- Henan Crop Molecular Design Breeding and Cultivation Engineering Technology Research Center, Zhoukou 466001, China
| | - Peiwen Li
- Henan Province Plant Genetics and Molecular Breeding Innovation Team, Zhoukou 466001, China; (F.M.); (P.L.); (M.J.); (S.L.); (J.L.); (M.Z.); (P.L.)
| | - Haiyan Guan
- Henan International Joint Laboratory of Translational Biology, Zhoukou 466001, China;
| | - Yi Zhang
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University/Henan Key Laboratory of Crop Molecular Breeding & Bioreactor, Zhoukou 466001, China; (D.W.); (J.W.); (M.M.)
- Henan International Joint Laboratory of Translational Biology, Zhoukou 466001, China;
| | - Hao Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, College of Agriculture, Henan University, Kaifeng 475000, China;
| |
Collapse
|
|
3
|
Li Z, Luo Q, Gan Y, Li X, Ou X, Deng Y, Fu S, Tang Z, Tan F, Luo P, Ren T. Identification and validation of major and stable quantitative trait locus for falling number in common wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:83. [PMID: 38491113 DOI: 10.1007/s00122-024-04588-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
KEY MESSAGE A major and stable QTL, QFn.sau-1B.2, which can explain 13.6% of the PVE in FN and has a positive effect on resistance in SGR, was mapped and validated. The falling number (FN) is considered one of the most important quality traits of wheat grain and is the most important quality evaluation index for wheat trade worldwide. The quantitative trait loci (QTLs) for FN were mapped in three years of experiments. 23, 30, and 58 QTLs were identified using the ICIM-BIP, ICIM-MET, and ICIM-EPI methods, respectively. Among them, seven QTLs were considered stable. QFn.sau-1B.2, which was mapped to the 1BL chromosome, can explain 13.6% of the phenotypic variation on average and is considered a major and stable QTL for FN. This QTL was mapped in a 1 cM interval and is flanked by the markers AX-110409346 and AX-108743901. Epistatic analysis indicated that QFN.sau-1B.2 has a strong influence on FN through both additive and epistatic effects. The Kompetitive Allele-Specific PCR marker KASP-AX-108743901, which is closely linked to QFn.sau-1B.2, was designed. The genetic effect of QFn.sau-1B.2 on FN was successfully confirmed in Chuannong18 × T1208 and CN17 × CN11 populations. Moreover, the results of the additive effects of favorable alleles for FN showed that the QTLs for FN had significant effects not only on FN but also on the resistance to spike germination. Within the interval of QFn.sau-1B.2, 147 high-confidence genes were found. According to the gene annotation and the transcriptome data, four genes might be associated with FN. QFn.sau-1B.2 may provide a new resource for the high-quality breeding of wheat in the future.
Collapse
Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Qinyi Luo
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yujie Gan
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xinli Li
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Xia Ou
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Yawen Deng
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Shulan Fu
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Zongxiang Tang
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Feiquan Tan
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Peigao Luo
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China
| | - Tianheng Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- College of Agronomy, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, Sichuan, China.
- Key Laboratory of Plant Genetics and Breeding at, Sichuan Agricultural University of Sichuan Province, Wenjiang, Chengdu, 611130, Sichuan, China.
| |
Collapse
|
|
4
|
Li Z, Luo Q, Deng Y, Du K, Li X, Ren T. Identification and Validation of a Stable Major-Effect Quantitative Trait Locus for Kernel Number per Spike on Chromosome 2D in Wheat ( Triticum aestivum L.). Int J Mol Sci 2023; 24:14289. [PMID: 37762591 PMCID: PMC10531874 DOI: 10.3390/ijms241814289] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 09/29/2023] Open
Abstract
A recombinant inbred line population including 371 lines was developed by a high kernel number per spike (KNPS) genotype T1208 and a low KNPS genotype Chuannong18 (CN18). A genetic linkage map consisting of 11,583 markers was constructed by the Wheat55K SNP Array. The quantitative trait loci (QTLs) related to KNPS were detected in three years. Eight, twenty-seven, and four QTLs were identified using the ICIM-BIP, ICIM-MET, and ICIM-EPI methods, respectively. One QTL, QKnps.sau-2D.1, which was mapped on chromosome 2D, can explain 18.10% of the phenotypic variation (PVE) on average and be considered a major and stable QTL for KNPS. This QTL was located in a 0.89 Mb interval on chromosome 2D and flanked by the markers AX-109283238 and AX-111606890. Moreover, KASP-AX-111462389, a Kompetitive Allele-Specific PCR (KASP) marker which closely linked to QKnps.sau-2D.1, was designed. The genetic effect of QKnps.sau-2D.1 on KNPS was successfully confirmed in two RIL populations. The results also showed that the significant increase of KNPS and 1000-kernel weight (TKW) was caused by QKnps.sau-2D.1 overcoming the disadvantage due to the decrease of spike number (SN) and finally lead to a significant increase of grain yield. In addition, within the interval in which QKnps.sau-2D.1 is located in Chinese Spring reference genomes, only fifteen genes were found, and two genes that might associate with KNPS were identified. QKnps.sau-2D.1 may provide a new resource for the high-yield breeding of wheat in the future.
Collapse
Affiliation(s)
- Zhi Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Qinyi Luo
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Yawen Deng
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Ke Du
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Xinli Li
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| | - Tianheng Ren
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China;
- College of Agronomy, Sichuan Agricultural University, Chengdu 611130, China; (Q.L.); (Y.D.); (K.D.); (X.L.)
- Key Laboratory of Plant Genetics and Breeding at Sichuan Agricultural University of Sichuan Province, Chengdu 611130, China
| |
Collapse
|
|
5
|
Guo G, Xu S, Chen H, Hao Y, Mao H. QTL Mapping for Wheat Seed Dormancy in a Yangmai16/Zhongmai895 Double Haploid Population. PLANTS (BASEL, SWITZERLAND) 2023; 12:759. [PMID: 36840107 PMCID: PMC9967201 DOI: 10.3390/plants12040759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/04/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
Pre-harvest sprouting (PHS) of wheat reduces grain yield and quality, and it is strongly affected by seed dormancy. Therefore, identification of quantitative trait loci (QTL) for seed dormancy is essential for PHS resistance breeding. A doubled haploid (DH) population, consisting of 174 lines from the cross between Yangmai16 (YM16) and Zhongmai895 (ZM895) was used to detect QTLs for seed dormancy and grain color. For seed dormancy, a total of seven QTLs were detected on chromosomes 2A, 3A, 3D, 4D, 5B and 5D over four environments, among which Qdor.hzau-3A, Qdor.hzau-3D.1 and Qdor.hzau-3D.2 were stably detected in more than two environments. For grain color, only two QTLs, Qgc.hzau-3A and Qgc.hzau-3D were detected on chromosomes 3A and 3D, which physically overlapped with Qdor.hzau-3A and Qdor.hzau-3D.1, respectively. Qdor.hzau-3D.2 has never been reported elsewhere and is probably a novel locus with allelic effect of seed dormancy contributed by weakly dormant parent ZM895, and a KASP marker was developed and validated in a wheat natural population. This study provides new information on the genetic dissection of seed dormancy, which may aid in further improvement for marker-assisted wheat breeding for PHS resistance.
Collapse
Affiliation(s)
- Gang Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shuhao Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing 100081, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|