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Xu H, Wang Z, Wang F, Hu X, Ma C, Jiang H, Xie C, Gao Y, Ding G, Zhao C, Qin R, Cui D, Sun H, Cui F, Wu Y. Genome-wide association study and genomic selection of spike-related traits in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:131. [PMID: 38748046 DOI: 10.1007/s00122-024-04640-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/27/2024] [Indexed: 06/09/2024]
Abstract
KEY MESSAGE Identification of 337 stable MTAs for wheat spike-related traits improved model accuracy, and favorable alleles of MTA259 and MTA64 increased grain weight and yield per plant. Wheat (Triticum aestivum L.) is one of the three primary global, staple crops. Improving spike-related traits in wheat is crucial for optimizing spike and plant morphology, ultimately leading to increased grain yield. Here, we performed a genome-wide association study using a dataset of 24,889 high-quality unique single-nucleotide polymorphisms (SNPs) and phenotypic data from 314 wheat accessions across eight diverse environments. In total, 337 stable and significant marker-trait associations (MTAs) related to spike-related traits were identified. MTA259 and MTA64 were consistently detected in seven and six environments, respectively. The presence of favorable alleles associated with MTA259 and MTA64 significantly reduced wheat spike exsertion length and spike length, while enhancing thousand kernel weight and yield per plant. Combined gene expression and network analyses identified TraesCS6D03G0692300 and TraesCS6D03G0692700 as candidate genes for MTA259 and TraesCS2D03G0111700 and TraesCS2D03G0112500 for MTA64. The identified MTAs significantly improved the prediction accuracy of each model compared with using all the SNPs, and the random forest model was optimal for genome selection. Additionally, the eight stable and major MTAs, including MTA259, MTA64, MTA66, MTA94, MTA110, MTA165, MTA180, and MTA164, were converted into cost-effective and efficient detection markers. This study provided valuable genetic resources and reliable molecular markers for wheat breeding programs.
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Affiliation(s)
- Huiyuan Xu
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Zixu Wang
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Faxiang Wang
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Xinrong Hu
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Chengxue Ma
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Huijiao Jiang
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Chang Xie
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Yuhang Gao
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Guangshuo Ding
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Chunhua Zhao
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Ran Qin
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China
| | - Dezhou Cui
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Key Laboratory of Wheat Biology and Genetics and Breeding in Northern Huang-Huai River Plain, Ministry of Agriculture and Rural Affairs/Shandong Technology Innovation Center of Wheat/Jinan Key Laboratory of Wheat Genetic Improvement, Jinan, Shandong, China
| | - Han Sun
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China.
| | - Fa Cui
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China.
| | - Yongzhen Wu
- College of Agriculture, Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, Shandong, China.
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Jia Y, Zhang Y, Sun Y, Ma C, Bai Y, Zhang H, Hou J, Wang Y, Ji W, Bai H, Hao S, Wang Z. QTL Mapping of Yield-Related Traits in Tetraploid Wheat Based on Wheat55K SNP Array. PLANTS (BASEL, SWITZERLAND) 2024; 13:1285. [PMID: 38794355 PMCID: PMC11125051 DOI: 10.3390/plants13101285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/01/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024]
Abstract
To enhance the understanding of yield-related traits in tetraploid wheat, it is crucial to investigate and identify genes that govern superior yield characteristics. This study utilized the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line (RIL) population consisting of 120 lines developed through the crossbreeding of two tetraploid wheat varieties, Qin Hei-1 (QH-1) and Durum Wheat (DW). An investigation and analysis were conducted on 11 yield-related traits, including peduncle length (PL), neck length (NL), spike length (SL), flowering date (FD), heading date (HD), thousand-kernel weight (TKW), kernel area ratio (KAR), kernel circumference (KC), kernel length (KL), kernel width (KW), and kernel length-width ratio (KL-WR), over a period of three years in two locations, Yang Ling, Shaanxi, and Lin He, Inner Mongolia. The analysis identified nine stable loci among eight agronomic traits, named QSL.QD-1A.1, QNL.QD-4B.2, QPL.QD-4B.1, QFD.QD-2B, QHD.QD-2B.1, QHD.QD-4B, QKC.QD-4B.2, QKL-WR.QD-4B.6, and QKL.QD-4B.2. Among them, the additive effects of three QTLs, QSL.QD-1A.1, QNL.QD-4B.2, and QFD.QD-2B, were positive, indicating that the enhancing alleles at these loci were derived from the parent line QH-1. These three QTLs showed significant positive effects on the phenotypes of the population materials. Furthermore, potential functional genes were identified within the mapping intervals of QSL.QD-1A.1 and QNL.QD-4B.2, which regulate the development of spike length and neck length, respectively. These results provide potential QTLs and candidate genes, which broaden the genetic basis of agronomic traits related to yield, such as SL, NL, PL, and FD, and benefits for wheat breeding and improvement.
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Affiliation(s)
- Yatao Jia
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Yifan Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Yingkai Sun
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Chao Ma
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Yixiong Bai
- Qinghai Key Laboratory of Hulless Barley Genetics and Breeding, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining 810016, China;
| | - Hanbing Zhang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Junbin Hou
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Yong Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Wanquan Ji
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
| | - Haibo Bai
- Agricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, China;
| | - Shuiyuan Hao
- Department of Agriculture, Hetao College, Bayan Nur City 015000, China
| | - Zhonghua Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling 712100, China; (Y.J.); (Y.Z.); (Y.S.); (C.M.); (H.Z.); (J.H.); (Y.W.); (W.J.)
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Zhang X, Xing P, Lin C, Wang H, Bao Y, Li X. QTL mapping for the flag leaf-related traits using RILs derived from Trititrigia germplasm line SN304 and wheat cultivar Yannong15 in multiple environments. BMC PLANT BIOLOGY 2024; 24:297. [PMID: 38632517 PMCID: PMC11025246 DOI: 10.1186/s12870-024-04993-x] [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: 11/01/2023] [Accepted: 04/08/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Developing and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits. RESULTS QTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified. CONCLUSION These results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.
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Affiliation(s)
- Xia Zhang
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Piyi Xing
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Caicai Lin
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, Shandong, 253023, China
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Honggang Wang
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Yinguang Bao
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Xingfeng Li
- National Key Laboratory of Wheat Improvement, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
- Tai'an Subcenter of the National Wheat Improvement Center, Agronomy College, Shandong Agricultural University, Tai'an, Shandong, 271018, China.
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Xu X, Su Y, Yang J, Li J, Gao Y, Li C, Wang X, Gou L, Zheng Z, Xie C, Ma J, Ma J. A novel QTL conferring Fusarium crown rot resistance on chromosome 2A in a wheat EMS mutant. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:49. [PMID: 38349579 DOI: 10.1007/s00122-024-04557-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024]
Abstract
KEY MESSAGE A novel QTL on chromosome 2A for Fusarium crown rot resistance was identified and validated in wheat. Fusarium crown rot (FCR) is a fungal disease that causes significant yield losses in many cereal growing regions in the world. In this study, genetic analysis was conducted for a wheat EMS mutant C549 which showed stable resistance to FCR at seedling stage. A total of 10 QTL were detected on chromosomes 1A, 2A, 3B, 4A, 6B, and 7B using a population of 138 F7 recombinant inbred lines (RILs) derived from a cross between C549 and a Chinese germplasm 3642. A novel locus Qfcr.cau-2A, which accounted for up to 24.42% of the phenotypic variation with a LOD value of 12.78, was consistently detected across all six trials conducted. Furthermore, possible effects of heading date (HD) and plant height on FCR severity were also investigated in the mapping population. While plant height had no effects on FCR resistance, a weak and negative association between FCR resistance and HD was observed. A QTL for HD (Qhd.cau-2A.2) was coincident with Qfcr.cau-2A. Conditional QTL mapping indicated that although Qfcr.cau-2A and Qhd.cau-2A.2 had significant interactions, Qfcr.cau-2A remained significant after the effects of HD was removed. It is unlikely that genes underlying these two loci are same. Nevertheless, the stable expression of Qfcr.cau-2A in the validation population of 148 F7 RILs developed between C549 and its wild parent Chuannong 16 demonstrated the potential value of this locus in FCR resistance breeding programs.
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Affiliation(s)
- Xiangru Xu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yuqing Su
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jiatian Yang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jinlong Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xingyi Wang
- College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Lulu Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhi Zheng
- CSIRO Agriculture and Food, Canberra, ACT, 2601, Australia
| | - Chaojie Xie
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Liu H, Zou Y, Xuan Q, Tian R, Zhu J, Qu X, Sun M, Liu Y, Tang H, Deng M, Jiang Q, Xu Q, Peng Y, Chen G, Li W, Pu Z, Jiang Y, Wang J, Qi P, Zhang Y, Zheng Y, Wei Y, Ma J. Loss of ADP-glucose transporter in barley sex1 mutant caused shrunken endosperm but with elevated protein and β-glucan content in whole meal. Int J Biol Macromol 2023; 251:126365. [PMID: 37591421 DOI: 10.1016/j.ijbiomac.2023.126365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/19/2023]
Abstract
Grain shape and plumpness affect barley yield. Despite numerous studies on shrunken endosperm mutants in barley, their molecular mechanism and application potential in the food industry are largely unknown. Here, map-based cloning, co-segregation analyses, and allelic variant validation revealed that the loss of HORVU6Hr1G037950 encoding an ADP-glucose transporter caused the shrunken endosperm in sex1. Haplotype analysis suggested that hap4 in the promoter sequence was positively related to the hundred-grain weight showing a breeding potential. A pair of near-isogenic lines targeting HORVU6Hr1G037950 was produced and characterized to investigate molecular mechanisms that SEX1 regulates endosperm development. Results presented that the absence of the SEX1 gene led to the decrease of starch content and A-type granules size, the increase of β-glucan, protein, gelatinization temperature, soluble sugar content, amylopectin A chains, and B1 chains. Enzymatic activity, transcriptome and metabolome analyses revealed the loss of SEX1 results in an impaired ADP-glucose-to-starch conversion process, consequently leading to higher soluble sugar contents and lower starch accumulation, thereby inducing a shrunken-endosperm phenotype in sex1. Taken together, this study provides new insights into barley grain development, and the elevated protein and β-glucan contents of the whole meal in sex1 imply its promising application in the food industry.
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Affiliation(s)
- Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaya Zou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China; Yan'an Academy of Agricultural Sciences, Yan'an, China
| | - Qijing Xuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Rong Tian
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Min Sun
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfi Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China; Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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Zhang Y, Miao H, Xiao Y, Wang C, Zhang J, Shi X, Xie S, Wang C, Li T, Deng P, Chen C, Zhang H, Ji W. An intron-located single nucleotide variation of TaGS5-3D is related to wheat grain size through accumulating intron retention transcripts. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:193. [PMID: 37606787 DOI: 10.1007/s00122-023-04439-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023]
Abstract
KEY MESSAGE Thirty-three stable QTL for 13 yield-related traits across ten environments were identified in the PD34/MY47 RIL population, and a candidate gene TaGS5-3D in Qmt.nwafu.3D was preliminarily identified to affect grain-related traits through accumulation of specific transcripts. Dissecting the genetic basis of yield-related traits is pivotal for improvement of wheat yield potential. In this study, a recombinant inbred line (RIL) population genotyped by SNP markers was used to detect quantitative trait loci (QTL) related to yield-related traits in ten environments. A total of 102 QTL were detected, including 33 environmentally stable QTL and 69 putative QTL. Among them, Qmt.nwafu.3D was identified as a pleiotropic QTL in the physical interval of 149.77-154.11 Mb containing a potential candidate gene TaGS5-3D. An SNP (T > C) was detected in its ninth intron, and TaGS5-3D-C was validated as a superior allele associated with larger grains using a CAPS marker. Interestingly, we found that TaGS5-3D-C was closely related to significantly up-regulated expression of intron-retained transcript (TaGS5-3D-PD34.1), while TaGS5-3D-T was related to dominant expression of normal splicing transcript (TaGS5-3D-MY47.1). Our results indicated that alternative splicing associated with the SNP T/C could be involved in the regulation of grain-related traits, laying a foundation for the functional analysis of TaGS5-3D and its greater potential application in high-yield wheat breeding.
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Affiliation(s)
- Yaoyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Hanxiao Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Yi Xiao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Xiaoxi Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Songfeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, China.
- Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs, Yangling, 712100, China.
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7
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Zhou J, Li W, Yang Y, Xie X, Liu J, Liu Y, Tang H, Deng M, Xu Q, Jiang Q, Chen G, Qi P, Jiang Y, Chen G, He Y, Ren Y, Tang L, Gou L, Zheng Y, Wei Y, Ma J. A promising QTL QSns.sau-MC-3D.1 likely superior to WAPO1 for the number of spikelets per spike of wheat shows no adverse effects on yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:181. [PMID: 37550493 DOI: 10.1007/s00122-023-04429-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 07/24/2023] [Indexed: 08/09/2023]
Abstract
KEY MESSAGE A likely new locus QSns.sau-MC-3D.1 associated with SNS showing no negative effect on yield-related traits compared to WAPO1 was identified and validated in various genetic populations under multiple environments. The number of spikelets per spike (SNS) is one of the crucial factors determining wheat yield. Thus, improving our understanding of the genes that regulate SNS could help develop wheat varieties with higher yield. In this study, a recombinant inbred line (RIL) population (MC) containing 198 lines derived from a cross between msf and Chuannong 16 (CN16) was used to construct a genetic linkage map using the GenoBaits Wheat 16 K Panel. The genetic map contained 5,991 polymorphic SNP markers spanning 2,813.25 cM. A total of twelve QTL for SNS were detected, and two of them, i.e., QSns.sau-MC-3D.1 and QSns.sau-MC-7A, were stably expressed. QSns.sau-MC-3D.1 had high LOD values ranging from 4.99 to 11.06 and explained 9.71-16.75% of the phenotypic variation. Comparison of QSns.sau-MC-3D.1 with previously reported SNS QTL suggested that it is likely a novel one, and two kompetitive allele-specific PCR (KASP) markers were further developed. The positive effect of QSns.sau-MC-3D.1 was also validated in three biparental populations and a diverse panel containing 388 Chinese wheat accessions. Genetic analysis indicated that WHEAT ORTHOLOG OFAPO1 (WAPO1) was a candidate gene for QSns.sau-MC-7A. Pyramiding of QSns.sau-MC-3D.1 and WAP01 had a great additive effect increasing SNS by 7.10%. Correlation analysis suggested that QSns.sau-MC-3D.1 was likely independent of effective tiller number, plant height, spike length, anthesis date, and thousand kernel weight. However, the H2 haplotype of WAPO1 may affect effective tiller number and plant height. These results indicated that utilization of QSns.sau-MC-3D.1 should be given priority for wheat breeding. Geographical distribution analysis showed that the positive allele of QSns.nsau-MC-3D.1 was dominant in most wheat-producing regions of China, and it has been positively selected among modern cultivars released in China since the 1940s. Gene prediction, qRT-PCR analysis, and sequence alignment suggested that TraesCS3D03G0216800 may be the candidate gene of QSns.nsau-MC-3D.1. Taken together, these results enrich our understanding of the genetic basis of wheat SNS and will be useful for fine mapping and cloning of the gene underlying QSns.sau-MC-3D.1.
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Affiliation(s)
- Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Yong Ren
- Mianyang Academy of Agricultural Science, Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China.
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8
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Wang M, Lu J, Liu R, Li Y, Ao D, Wu Y, Zhang L. Identification and validation of a major quantitative trait locus for spike length and compactness in the wheat ( Triticum aestivum L.) line Chuanyu12D7. FRONTIERS IN PLANT SCIENCE 2023; 14:1186183. [PMID: 37469784 PMCID: PMC10353862 DOI: 10.3389/fpls.2023.1186183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
Spike length (SL) and spike compactness (SC) are crucial traits related to wheat (Triticum aestivum L.) yield potential. In this study, a backcrossed inbred lines (BILs) population segregating for SL/SC was developed by using a commercial variety chuanyu25 as recurrent parent and a backbone parent Chuanyu12D7. Bulked segregant analysis (BSA) combined with the Wheat 660K SNP array was performed to conduct quantitative trait locus (QTL) mapping. A major and stable SL/SC QTL (designated as QSl/Sc.cib-2D.1) was identified on chromosome 2DS, explaining 45.63-59.72% of the phenotypic variation. QSl/Sc.cib-2D.1 was mapped to a 102.29-Kb interval by flanking SNPs AX-110276364 and AX-111593853 using a BC4F2:3 population. Since QSl/Sc.cib-2D.1 is linked to the Rht8 gene, their additive effects on plant type and spike type were analysed. Remarkably, the superior allele of QSl/Sc.cib-2D.1 combined with Rht8 can increase SL and TGW, and decrese SC without any apparent trade-offs in other yield-related traits. In addition, the closely linked kompetitive allele-specific PCR (KASP) markers of this locus were developed for marker-assisted selection (MAS) breeding. Four genes within the physical interval were considered as potential candidates based on expression patterns as well as orthologous gene functions. These results laid the foundation for map-based cloning of the gene(s) underlying QSl/Sc.cib-2D.1 and its potential application in wheat ideotype breeding.
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Affiliation(s)
- Mingxiu Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Lu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rong Liu
- Department of Agriculture, Forestry and Food Engineering of Yibin University, Yibin, China
| | - Yunfang Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Donghui Ao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Yu Wu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lei Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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9
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Tang H, Dong H, Guo X, Cheng M, Li M, Chen Q, Yuan Z, Pu Z, Wang J. Identification of candidate gene for the defective kernel phenotype using bulked segregant RNA and exome capture sequencing methods in wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1173861. [PMID: 37342127 PMCID: PMC10277647 DOI: 10.3389/fpls.2023.1173861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 05/03/2023] [Indexed: 06/22/2023]
Abstract
Wheat is a significant source of protein and starch worldwide. The defective kernel (Dek) mutant AK-3537, displaying a large hollow area in the endosperm and shrunken grain, was obtained through ethyl methane sulfonate (EMS) treatment of the wheat cultivar Aikang 58 (AK58). The mode of inheritance of the AK-3537 grain Dek phenotype was determined to be recessive with a specific statistical significance level. We used bulked segregant RNA-seq (BSR-seq), BSA-based exome capture sequencing (BSE-seq), and the ΔSNP-index algorithm to identify candidate regions for the grain Dek phenotype. Two major candidate regions, DCR1 (Dek candidate region 1) and DCR2, were identified on chromosome 7A between 279.98 and 287.93 Mb and 565.34 and 568.59 Mb, respectively. Based on transcriptome analysis and previous reports, we designed KASP genotyping assays based on SNP variations in the candidate regions and speculated that the candidate gene is TraesCS7A03G0625900 (HMGS-7A), which encodes a 3-hydroxy-3-methylglutaryl-CoA synthase. One SNP variation located at position 1,049 in the coding sequence (G>A) causes an amino acid change from Gly to Asp. The research suggests that functional changes in HMGS-7A may affect the expression of key enzyme genes involved in wheat starch syntheses, such as GBSSII and SSIIIa.
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Affiliation(s)
- Hao Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Huixue Dong
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Xiaojiang Guo
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Mengping Cheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Maolian Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Qian Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhongwei Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Ministry of Education Key Laboratory for Crop Genetic Resources and Improvement in Southwest China, Sichuan Agricultural University, Chengdu, China
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10
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Wang S, Wang T, Xuan Q, Qu X, Xu Q, Jiang Q, Pu Z, Li Y, Jiang Y, Chen G, Deng M, Liu Y, Tang H, Chen G, He Y, Gou L, Wei Y, Zheng Y, Ma J. Major and stably expressed QTL for traits related to the mature wheat embryo independent of kernel size. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:90. [PMID: 37000252 DOI: 10.1007/s00122-023-04346-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Two major and stably expressed QTL for traits related to mature wheat embryo independent of kernel size were identified and validated in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. As the juvenile of a highly differentiated plant, mature wheat (Triticum aestivum L.) embryos are highly significant to agricultural production. To understand the genetic basis of traits related to wheat embryo size, the embryo of mature kernels in a recombination inbred line that contained 126 lines from four environments was measured. The genetic loci of embryo size, including embryo length (EL), embryo width (EW), embryo area (EA), embryo length/kernel length (EL/KL), embryo width/kernel width (EW/KW), and EL/EW, were identified based on a genetic linkage map constructed based on PCR markers and the Wheat 55 K single nucleotide polymorphism (SNP) array. A total of 50 quantitative trait loci (QTL) for traits related to wheat embryo size were detected. Among them, QEL.sicau-2SY-4A for EL and QEW.sicau-2SY-7B for EW were major and stably expressed and were genetically independent of KL and KW, respectively. Their effects were further verified in a natural population that contained 171 Sichuan wheat accessions and 49 Sichuan wheat landraces. Further analysis showed that TraesCS4A02G343300 and TraesCS7B02G006800 could be candidate genes for QEL.sicau-2SY-4A and QEW.sicau-2SY-7B, respectively. In addition, significant positive correlations between EL and kernel-related traits and the 1,000-grain weight were detected. Collectively, this study broadens our understanding of the genetic basis of wheat embryo size and will be helpful for the further fine-mapping of interesting loci in the future.
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Affiliation(s)
- Surong Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tianyu Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qijing Xuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yanling Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuanjiang He
- Mianyang Academy of Agricultural Science/Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Providence, Mianyang, 621000, China
| | - Lulu Gou
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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11
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Liu Z, Zhao P, Lai X, Wang X, Ji W, Xu S. The selection and application of peduncle length QTL QPL_6D.1 in modern wheat (Triticum aestivum L.) breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:32. [PMID: 36897424 DOI: 10.1007/s00122-023-04274-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
QPL_6D.1b displayed an additive effect with Rht-B1b and Rht-D1b in reducing wheat plant height and peduncle length, which confers shorter peduncle length and more kernels per spike, and had been broadly selected by Chinese modern wheat cultivars. Peduncle length (PL), as the key component of wheat plant height (PH), plays critical role in determining wheat lodging resistance and wheat pathogen resistance; then, its breeding selection and genetic basis remain largely unclear. Here the PH and PL were investigated in 406 wheat accessions in eight environments. In this study, a PL preferentially QTL QPL_6D.1 was identified in six environments by GWAS, which explained 13.6-24.2% of wheat PL variations in natural population. The allele QPL_6D.1b displayed a significantly additive effect with Rht-B1b and Rht-D1b in controlling PH and PL and could freely combined with Rht-B1b and Rht-D1b in current wheat cultivars. Haplotypic analysis demonstrates the QPL_6D.1b has been selected by Chinese modern wheat cultivar and confers shorter PL and more kernels per spike, highlighting its potentials in wheat breeding.
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Affiliation(s)
- Zihui Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Peng Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiangjun Lai
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Xiaoming Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Shengbao Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, 712100, Shaanxi, People's Republic of China.
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12
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Qiao L, Zhang X, Li X, Yang Z, Li R, Jia J, Yan L, Chang Z. Genetic incorporation of genes for the optimal plant architecture in common wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:66. [PMID: 37313009 PMCID: PMC10248654 DOI: 10.1007/s11032-022-01336-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 10/03/2022] [Indexed: 06/15/2023]
Abstract
Wheat grain yield is affected by plant height, which is the total length of spike, the uppermost internode, and other elongated internodes. In this study, a population of recombinant inbred lines generated from a cross between two advanced winter wheat breeding lines were phenotyped over four locations/years and genotyped by using markers of genotyping-by-sequencing (GBS) and Diversity Array Technology (DArT) for mapping of genes for three traits, including spike length, the uppermost internode length, and plant height. Five genomic regions or quantitative trait loci (QTLs) were associated with candidate genes for these traits. A major QTL was associated with Q5A, and two novel haplotypes of Q5A were identified, one for a single nucleotide polymorphism (SNP) at position -2,149 in promoter region and the other for copy number variation. Compared with one copy Q5A on chromosome 5A in Chinese Spring, the novel haplotype of Q5A with two copies Q5A was found to generate spikes that are extremely compacted. A major QTL was associated with allelic variation in the recessive vrn-A1 alleles involving in protein sequences, and this QTL was associated with increased uppermost internode length but not with plant height. A major QTL for plant height was associated with Rht-B1b on chromosome 4B, but its effects could be compromised by two new minor QTLs on chromosome 7. Collectively, the favorable alleles from the four loci can be used to establish the optimal plant height in wheat. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01336-2.
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Affiliation(s)
- Linyi Qiao
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078 USA
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Xin Li
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Zujun Yang
- School of Life Science and Technology, Science and Technology of China, University of Electronic, Chengdu, 610054 China
| | - Rui Li
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Juqing Jia
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
| | - Liuling Yan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK 74078 USA
| | - Zhijian Chang
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031 Shanxi China
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13
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Chen H, Zhao C, Yang Y, Zeng Z, Li W, Liu Y, Tang H, Xu Q, Deng M, Jiang Q, Chen G, Peng Y, Jiang Y, Jiang Y, Wei Y, Zheng Y, Lan X, Ma J. Identification and validation of a locus for wheat maximum root length independent of parental reproductive environment. FRONTIERS IN PLANT SCIENCE 2022; 13:999414. [PMID: 36172559 PMCID: PMC9511226 DOI: 10.3389/fpls.2022.999414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Maximum root length (MRL) plays an important role in the uptake of nutrients and resisting abiotic stresses. Understanding the genetic mechanism of root development is of great significance for genetic improvement of wheat. Previous studies have confirmed that parental reproductive environment (PRE) has a significant impact on growth and development of the next generation in the whole life cycle of a given plant. In this study, a recombinant inbred line population genotyped using the Wheat55K SNP array, was used to map quantitative trait loci (QTL) for wheat seedling MRL based on the harvested seeds from five different PREs. A total of 5 QTL located on chromosomes 3D and 7A were identified. Among them, QMrl.sicau-2SY-3D.2 located in a 4.0 cM interval on chromosome 3D was likely independent of PREs. QMrl.sicau-2SY-7A.2 was detected in two tests and probably influenced by PREs. The effect of QMrl.sicau-2SY-3D.2 was further validated using the tightly linked kompetitive allele specific PCR (KASP) marker, KASP-AX-111589572, in populations with different genetic backgrounds. Lines with a combination of positive alleles from QMrl.sicau-2SY-3D.2 and QMrl.sicau-2SY-7A.2 have significantly longer MRL. Furthermore, four genes (TraesCS3D03G0612000, TraesCS3D03G0608400, TraesCS3D03G0613600, and TraesCS3D03G0602400) mainly expressed in wheat root were predicted to be associated with root growth. Taken together, this study reports on a major QTL independent of PREs and lays a foundation for understanding the regulation mechanism of wheat MRL at the seedling stage.
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Affiliation(s)
- Huangxin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhaoyong Zeng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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14
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Chen H, Wei J, Tian R, Zeng Z, Tang H, Liu Y, Xu Q, Deng M, Jiang Q, Chen G, Liu Y, Li W, Qi P, Jiang Y, Jiang Y, Tang L, Wei Y, Zheng Y, Lan X, Ma J. A major quantitative trait locus for wheat total root length associated with precipitation distribution. FRONTIERS IN PLANT SCIENCE 2022; 13:995183. [PMID: 36092437 PMCID: PMC9451531 DOI: 10.3389/fpls.2022.995183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Optimizing root system architecture (RSA) allows crops to better capture water and nutrients and adapt to harsh environment. Parental reproductive environment (PRE) has been reported to significantly affect growth and development throughout the life cycle of the next generation. In this study, 10 RSA-related traits were evaluated in seedling stage from five independent hydroponic tests using seeds harvested from five different PREs. Based on the Wheat55K SNP array-based genetic map, quantitative trait loci (QTL) for these traits were detected in a recombinant inbred line population. Twenty-eight putative QTL for RSA-related traits were detected, covering thirteen chromosomal regions. A major QTL, QTrl.sicau-2SY-4D for total root length (TRL), which was likely independent of PREs, explained 15.81-38.48% of phenotypic variations and was located at 14.96-19.59 Mb on chromosome arm 4DS. Interestingly, it showed pleiotropic effects on TRL, root area, root volume, root forks, root dry weight, and shoot dry weight. The functional marker KASP-Rht-D1 for Rht-D1 was used to genotype 2SY population and remapping QTL for TRL showed that QTrl.sicau-2SY-4D was not linked to Rht-D1. The kompetitive allele-specific PCR (KASP) marker, KASP-AX-110527441 linked to this major QTL, was developed and used to successfully validate its effect in three different genetic populations. Further analysis suggested that the positive allele at QTrl.sicau-2SY-4D was mainly utilized in wheat breeding of northwest China where precipitation was significantly lower, indicating that wheat requires longer TRL to capture water and nutrients in arid or semi-arid regions due to deficient precipitation. Additionally, four genes (TraesCS4D03G0059800, TraesCS4D03G0057800, TraesCS4D03G0064000, and TraesCS4D03G0064400) possibly related to root development were predicted in physical interval of QTrl.sicau-2SY-4D. Taken together, these results enrich our understanding on the genetic basis of RSA and provide a potentially valuable TRL QTL for wheat breeding.
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Affiliation(s)
- Huangxin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Rong Tian
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhaoyong Zeng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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15
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Wei J, Fang Y, Jiang H, Wu XT, Zuo JH, Xia XC, Li JQ, Stich B, Cao H, Liu YX. Combining QTL mapping and gene co-expression network analysis for prediction of candidate genes and molecular network related to yield in wheat. BMC PLANT BIOLOGY 2022; 22:288. [PMID: 35698038 PMCID: PMC9190149 DOI: 10.1186/s12870-022-03677-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/27/2022] [Indexed: 05/21/2023]
Abstract
BACKGROUND Wheat (Triticum aestivum L.) is an important cereal crop. Increasing grain yield for wheat is always a priority. Due to the complex genome of hexaploid wheat with 21 chromosomes, it is difficult to identify underlying genes by traditional genetic approach. The combination of genetics and omics analysis has displayed the powerful capability to identify candidate genes for major quantitative trait loci (QTLs), but such studies have rarely been carried out in wheat. In this study, candidate genes related to yield were predicted by a combined use of linkage mapping and weighted gene co-expression network analysis (WGCNA) in a recombinant inbred line population. RESULTS QTL mapping was performed for plant height (PH), spike length (SL) and seed traits. A total of 68 QTLs were identified for them, among which, 12 QTLs were stably identified across different environments. Using RNA sequencing, we scanned the 99,168 genes expression patterns of the whole spike for the recombinant inbred line population. By the combined use of QTL mapping and WGCNA, 29, 47, 20, 26, 54, 46 and 22 candidate genes were predicted for PH, SL, kernel length (KL), kernel width, thousand kernel weight, seed dormancy, and seed vigor, respectively. Candidate genes for different traits had distinct preferences. The known PH regulation genes Rht-B and Rht-D, and the known seed dormancy regulation genes TaMFT can be selected as candidate gene. Moreover, further experiment revealed that there was a SL regulatory QTL located in an interval of about 7 Mbp on chromosome 7A, named TaSL1, which also involved in the regulation of KL. CONCLUSIONS A combination of QTL mapping and WGCNA was applied to predicted wheat candidate genes for PH, SL and seed traits. This strategy will facilitate the identification of candidate genes for related QTLs in wheat. In addition, the QTL TaSL1 that had multi-effect regulation of KL and SL was identified, which can be used for wheat improvement. These results provided valuable molecular marker and gene information for fine mapping and cloning of the yield-related trait loci in the future.
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Affiliation(s)
- Jun Wei
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Fang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Jiang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xing-Ting Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing-Hong Zuo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xian-Chun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jin-Quan Li
- Strube Research GmbH & Co., KG, 38387, S ̈ollingen, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Heinrich Heine University, D ̈usseldorf, Germany
| | - Hong Cao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yong-Xiu Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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16
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Li C, Liu H, Wang J, Pan Q, Wang Y, Wu K, Jia P, Mu Y, Tang H, Xu Q, Jiang Q, Liu Y, Qi P, Zhang X, Huang L, Chen G, Wang J, Wei Y, Zheng Y, Gou L, Yao Q, Lan X, Ma J. Characterization and fine mapping of a lesion mimic mutant (Lm5) with enhanced stripe rust and powdery mildew resistance in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:421-438. [PMID: 34661696 DOI: 10.1007/s00122-021-03973-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 10/08/2021] [Indexed: 06/13/2023]
Abstract
A novel light intensity-dependent lesion mimic mutant with enhanced disease resistance was physiologically, biochemically, and genetically characterized, and the causative gene was fine mapped to a 1.28 Mbp interval containing 17 high-confidence genes. Lesion mimic mutants are ideal for studying disease resistance and programmed cell death photosynthesis in plants to improve crop yield. In this study, a novel light intensity-dependent lesion mimic mutant (MC21) was obtained from the wheat variety Chuannong16 (CN16) by ethyl methane sulfonate treatment. The mutant initially developed tiny lesion spots on the basal part of the leaves, which then gradually proceeded down to leaf sheaths, stems, shells, and awns at the flowering stage. The major agronomic traits were significantly altered in the mutant compared to that in the wild-type CN16. Furthermore, the mutant exhibited a lesion phenotype with degenerated chloroplast structure, decreased chlorophyll content, increased level of reactive oxygen species, and increased resistance to stripe rust and powdery mildew. Genetic analysis indicated that the lesion phenotype was controlled by a novel single semi-dominant nuclear gene. The target gene was mapped on chromosome arm 2AL located between Kompetitive Allele Specific PCR (KASP) markers, KASP-4211 and KASP-5353, and tentatively termed as lesion mimic 5 (Lm5). The fine mapping suggested that Lm5 was located in a 1.28 Mbp interval between markers KASP-5825 and KASP-9366; 17 high-confidence candidate genes were included in this genomic region. This study provides an important foundational step for further cloning of Lm5 using a map-based approach.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hang Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qi Pan
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yue Wang
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kunyan Wu
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Peiying Jia
- College of Agronomy, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaojun Zhang
- College of Agronomy, Shanxi Agricultural University, Taiyuan, 030031, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lulu Gou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qifu Yao
- College of Agroforestry Engineering and Planning/Guizhou Key Laboratory of Biodiversity Conservation and Utilization in the Fanjing Mountain Region, Tongren University, Tongren, 554300, China.
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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17
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You J, Liu H, Wang S, Luo W, Gou L, Tang H, Mu Y, Deng M, Jiang Q, Chen G, Qi P, Peng Y, Tang L, Habib A, Wei Y, Zheng Y, Lan X, Ma J. Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations. FRONTIERS IN PLANT SCIENCE 2021; 12:796397. [PMID: 34975986 PMCID: PMC8716915 DOI: 10.3389/fpls.2021.796397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 11/26/2021] [Indexed: 05/15/2023]
Abstract
Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson's correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.
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Affiliation(s)
- Jianing You
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Hang Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Surong Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Luo
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lulu Gou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Yuming Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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18
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Pu X, Tang Y, Zhang M, Li T, Qiu X, Zhang J, Wang J, Li L, Yang Z, Su Y, Zhang H, Liang J, Yu M, Tang Y, Deng G, Long H. Identification and candidate gene mining of HvSS1, a novel qualitative locus on chromosome 6H, regulating the uppermost internode elongation in barley (Hordeum vulgare L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2481-2494. [PMID: 33942136 DOI: 10.1007/s00122-021-03837-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 04/13/2021] [Indexed: 05/27/2023]
Abstract
A novel qualitative locus regulating the uppermost internode elongation of barley was identified and mapped on 6H, and the candidate gene mining was performed by employing various barley genomic resources. The stem of grass crops, such as barley and wheat, is composed of several interconnected internodes. The extent of elongation of these internodes determines stem height, and hence lodging, canopy architecture, and grain yield. The uppermost internode (UI) is the last internode to elongate. Its elongation contributes largely to stem height and facilitates spike exsertion, which is crucial for final grain yield. Despite the molecular mechanism underlying regulation of UI elongation was extensively investigated in rice, little is known in barley. In this study, we characterized a barley spontaneous mutant, Sheathed Spike 1 (SS1), showing significantly shortened UI and sheathed spike (SS). The extension of UI parenchyma cell in SS1 was significantly suppressed. Exogenous hormone treatments and RNA-seq analysis indicated that the suppression of UI elongation is possibly related to insufficient content of endogenous bioactive gibberellin. Genetic analysis showed that SS1 is possibly controlled by a qualitative dominant nuclear factor. Bulked segregant analysis and further molecular marker mapping identified a novel major locus, HvSS1, in a recombination cold spot expanding 173.44-396.33 Mb on chromosome 6H. The candidate gene mining was further conducted by analyzing sequence differences, spatiotemporal expression patterns, and variant distributions of genes in the candidate interval by employing various barley genomic resources of worldwide collections of barley accessions. This study made insight into genetic control of UI elongation in barley and laid a solid foundation for further gene cloning and functional characterization. The results obtained here also provided valuable information for similar research in wheat.
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Affiliation(s)
- Xi Pu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yanyan Tang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Meihao Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Tao Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xvebing Qiu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Juanyu Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Jinhui Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Lilan Li
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Zhao Yang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yan Su
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Haili Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Junjun Liang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Maoqun Yu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Yawei Tang
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, People's Republic of China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People's Republic of China.
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19
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Khomenko S, Fedorenko M, Chugunkova T. Inheritance of Yield Components and Heterosis in Spring Durum Wheat Hybrids (Triticum durum Desf.). CYTOL GENET+ 2021. [DOI: 10.3103/s0095452721040058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Mo Z, Zhu J, Wei J, Zhou J, Xu Q, Tang H, Mu Y, Deng M, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Li W, Wei Y, Zheng Y, Lan X, Ma J. The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat ( Triticum turgidum L.) Population: Chinese Landrace "Ailanmai" × Wild Emmer. FRONTIERS IN PLANT SCIENCE 2021; 12:732837. [PMID: 34531890 PMCID: PMC8439258 DOI: 10.3389/fpls.2021.732837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/18/2021] [Indexed: 05/08/2023]
Abstract
Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace "Ailanmai" × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.
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Affiliation(s)
- Ziqiang Mo
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jing Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jieguang Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Xiujin Lan
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Jian Ma
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Ruan Y, Yu B, Knox RE, Zhang W, Singh AK, Cuthbert R, Fobert P, DePauw R, Berraies S, Sharpe A, Fu BX, Sangha J. Conditional Mapping Identified Quantitative Trait Loci for Grain Protein Concentration Expressing Independently of Grain Yield in Canadian Durum Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:642955. [PMID: 33841470 PMCID: PMC8024689 DOI: 10.3389/fpls.2021.642955] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 02/26/2021] [Indexed: 05/22/2023]
Abstract
Grain protein concentration (GPC) is an important trait in durum cultivar development as a major determinant of the nutritional value of grain and end-use product quality. However, it is challenging to simultaneously select both GPC and grain yield (GY) due to the negative correlation between them. To characterize quantitative trait loci (QTL) for GPC and understand the genetic relationship between GPC and GY in Canadian durum wheat, we performed both traditional and conditional QTL mapping using a doubled haploid (DH) population of 162 lines derived from Pelissier × Strongfield. The population was grown in the field over 5 years and GPC was measured. QTL contributing to GPC were detected on chromosome 1B, 2B, 3A, 5B, 7A, and 7B using traditional mapping. One major QTL on 3A (QGpc.spa-3A.3) was consistently detected over 3 years accounting for 9.4-18.1% of the phenotypic variance, with the favorable allele derived from Pelissier. Another major QTL on 7A (QGpc.spa-7A) detected in 3 years explained 6.9-14.8% of the phenotypic variance, with the beneficial allele derived from Strongfield. Comparison of the QTL described here with the results previously reported led to the identification of one novel major QTL on 3A (QGpc.spa-3A.3) and five novel minor QTL on 1B, 2B and 3A. Four QTL were common between traditional and conditional mapping, with QGpc.spa-3A.3 and QGpc.spa-7A detected in multiple environments. The QTL identified by conditional mapping were independent or partially independent of GY, making them of great importance for development of high GPC and high yielding durum.
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Affiliation(s)
- Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
- Yuefeng Ruan
| | - Bianyun Yu
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
- *Correspondence: Bianyun Yu
| | - Ron E. Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Wentao Zhang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Asheesh K. Singh
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Pierre Fobert
- Aquatic and Crop Resource Development, National Research Council Canada, Ottawa, ON, Canada
| | - Ron DePauw
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Samia Berraies
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Andrew Sharpe
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, SK, Canada
| | - Bin Xiao Fu
- Grain Research Laboratory, Canadian Grain Commission, Winnipeg, MB, Canada
| | - Jatinder Sangha
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
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22
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Qu X, Liu J, Xie X, Xu Q, Tang H, Mu Y, Pu Z, Li Y, Ma J, Gao Y, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Habib A, Wei Y, Zheng Y, Lan X, Ma J. Genetic Mapping and Validation of Loci for Kernel-Related Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:667493. [PMID: 34163507 PMCID: PMC8215603 DOI: 10.3389/fpls.2021.667493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 05/11/2023]
Abstract
Kernel size (KS) and kernel weight play a key role in wheat yield. Phenotypic data from six environments and a Wheat55K single-nucleotide polymorphism array-based constructed genetic linkage map from a recombinant inbred line population derived from the cross between the wheat line 20828 and the line SY95-71 were used to identify quantitative trait locus (QTL) for kernel length (KL), kernel width (KW), kernel thickness (KT), thousand-kernel weight (TKW), kernel length-width ratio (LWR), KS, and factor form density (FFD). The results showed that 65 QTLs associated with kernel traits were detected, of which the major QTLs QKL.sicau-2SY-1B, QKW.sicau-2SY-6D, QKT.sicau-2SY-2D, and QTKW.sicau-2SY-2D, QLWR.sicau-2SY-6D, QKS.sicau-2SY-1B/2D/6D, and QFFD.sicau-2SY-2D controlling KL, KW, KT, TKW, LWR, KS, and FFD, and identified in multiple environments, respectively. They were located on chromosomes 1BL, 2DL, and 6DS and formed three QTL clusters. Comparison of genetic and physical interval suggested that only QKL.sicau-2SY-1B located on chromosome 1BL was likely a novel QTL. A Kompetitive Allele Specific Polymerase chain reaction (KASP) marker, KASP-AX-109379070, closely linked to this novel QTL was developed and used to successfully confirm its effect in two different genetic populations and three variety panels consisting of 272 Chinese wheat landraces, 300 Chinese wheat cultivars most from the Yellow and Huai River Valley wheat region, and 165 Sichuan wheat cultivars. The relationships between kernel traits and other agronomic traits were detected and discussed. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified major QTL. Taken together, these stable and major QTLs provide valuable information for understanding the genetic composition of kernel yield and provide the basis for molecular marker-assisted breeding.
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Affiliation(s)
- Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Xiujin Lan,
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Jian Ma, ;
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