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Sertse D, Fetene A, Leon J, You FM, Cloutier S, McCartney CA. Tracing post-domestication historical events and screening pre-breeding germplasm from large gene pools in wheat in the absence of phenotype data. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:237. [PMID: 39340687 DOI: 10.1007/s00122-024-04738-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/04/2024] [Indexed: 09/30/2024]
Abstract
Wheat, particularly common wheat (Triticum aestivum L.), is a major crop accounting for 25% of the world cereal production and thriving in diverse ecogeographic regions. Its adaptation to diverse environments arises from its three distinct genomes adapted to different environments and post-domestication anthropogenic interventions. In search of key genomic regions revealing historic events and breeding significance to common wheat, we performed genome scan and genome-environment association (GEA) analyses using high-marker density genotype datasets. Whole-genome scans revealed highly differentiated regions on chromosomes 2A, 3B, and 4A. In-depth analyses corroborated our previous prediction of the 4A differentiated region signifying the separation between Spelt/Macha and other wheat types. Individual chromosome scans captured key introgressions, including one from T. timopheevii and one from Thinopyrum ponticum on 2B and 3D, respectively, as well as known genes such as Vrn-A1 on 5A. GEA highlighted loci linked to latitude-induced environmental variations, influencing traits such as photoperiodism and responses to abiotic stress. Variation at the Vrn-A1 locus on 5A assigned accessions to two haplotypes (6% and 94%). Further analysis on Vrn-A1 coding gene revealed four subgroups of the major haplotype, while the minor haplotype remained undifferentiated. Analyses at differentiated loci mostly dichotomized the population, illustrating the possibility of isolating pre-breeding materials with desirable traits from large gene pools in the absence of phenotype data. Given the current availability of broad genetic data, the genome-scan-GEA hybrid can be an efficient and cost-effective approach for pinpointing environmentally resilient pre-breeding germplasm from vast gene pools, including gene banks regardless of trait characterization.
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Affiliation(s)
- Demissew Sertse
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
| | - Aramde Fetene
- Department of Environmental Planning and Landscape Design, EiABC, Addis Ababa University, Addis Ababa, Ethiopia
| | - Jen Leon
- Department of Plant Breeding, University of Bonn, Bonn, Germany
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Sylvie Cloutier
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Curt A McCartney
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada.
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Mahmoud A, Qi R, Chi X, Liao N, Malangisha GK, Ali A, Moustafa-Farag M, Yang J, Zhang M, Hu Z. Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon. Int J Mol Sci 2023; 25:65. [PMID: 38203237 PMCID: PMC10779233 DOI: 10.3390/ijms25010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/07/2023] [Accepted: 12/09/2023] [Indexed: 01/12/2024] Open
Abstract
Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.
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Affiliation(s)
- Ahmed Mahmoud
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Rui Qi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Xiaolu Chi
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
| | - Nanqiao Liao
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Guy Kateta Malangisha
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Abid Ali
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
| | - Mohamed Moustafa-Farag
- Horticulture Research Institute, Agricultural Research Center, 9 Cairo University St, Giza 12619, Egypt;
| | - Jinghua Yang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Mingfang Zhang
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
| | - Zhongyuan Hu
- Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China; (A.M.); (R.Q.); (X.C.); (N.L.); (G.K.M.); (A.A.); (J.Y.); (M.Z.)
- Hainan Institute of Zhejiang University, Yazhou District, Sanya 572025, China
- Key Laboratory of Horticultural Plant Growth, Development & Quality Improvement, Ministry of Agriculture, Hangzhou 310058, China
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Valladares García AP, Desiderio F, Simeone R, Ravaglia S, Ciorba R, Fricano A, Guerra D, Blanco A, Cattivelli L, Mazzucotelli E. QTL mapping for kernel-related traits in a durum wheat x T. dicoccum segregating population. FRONTIERS IN PLANT SCIENCE 2023; 14:1253385. [PMID: 37849841 PMCID: PMC10577384 DOI: 10.3389/fpls.2023.1253385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.
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Affiliation(s)
- Ana Paola Valladares García
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Ciorba
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
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Ye M, Wan H, Yang W, Liu Z, Wang Q, Yang N, Long H, Deng G, Yang Y, Feng H, Zhou Y, Yang C, Li J, Zhang H. Precisely mapping a major QTL for grain weight on chromosome 5B of the founder parent Chuanmai42 in the wheat-growing region of southwestern China. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:146. [PMID: 37258797 DOI: 10.1007/s00122-023-04383-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
KEY MESSAGE QTgw.saas-5B was validated as a major thousand-grain weight-related QTL in a founder parent used for wheat breeding and then precisely mapped to a 0.6 cM interval. Increasing the thousand-grain weight (TGW) is considered to be one of the most important ways to improve yield, which is a core objective among wheat breeders. Chuanmai42, which is a wheat cultivar with high TGW and a high and stable yield, is a parent of more than 30 new varieties grown in southwestern China. In this study, a Chuanmai42-derived recombinant inbred line (RIL) population was used to dissect the genetic basis of TGW. A major QTL (QTgw.saas-5B) mapped to the Xgwm213-Xgwm540 interval on chromosome 5B of Chuanmai42 explained up to 20% of the phenotypic variation. Using 71 recombinants with a recombination in the QTgw.saas-5B interval identified from a secondary RIL population comprising 1818 lines constructed by crossing the QTgw.saas-5B near-isogenic line with the recurrent parent Chuannong16, QTgw.saas-5B was delimited to a 0.6 cM interval, corresponding to a 21.83 Mb physical interval in the Chinese Spring genome. These findings provide the foundation for QTgw.saas-5B cloning and its use in molecular marker-assisted breeding.
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Affiliation(s)
- Meijin Ye
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Qin Wang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China
| | - Ning Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China
| | - Hai Long
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Guangbing Deng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Yumin Yang
- Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Hong Feng
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
| | - Yonghong Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cairong Yang
- College of Chemistry and Life Sciences, Chengdu Normal University, Chengdu, 611130, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China (MARA), Chengdu, 610066, China.
- Environment-Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Chengdu, 610066, China.
| | - Haiqin Zhang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, 611130, China.
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Yang Y, Kong Z, Xie Q, Jia H, Huang W, Zhang L, Cheng R, Yang Z, Qi X, Lv G, Zhang Y, Wen Y, Ma Z. Fine mapping of KLW1 that conditions kernel weight mainly through regulating kernel length in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:110. [PMID: 37039971 DOI: 10.1007/s00122-023-04353-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
KLW1 was localized to a 0.6 cM interval near the centromere of chromosome 4B and found to be dominant in conditioning longer kernels and higher kernel weight. Kernel weight is a major wheat yield component and affected by kernel dimensions, filling process and kernel density. Because of this complexity, the mechanism underlying kernel weight is still far from clear. Qtgw.nau-4B or KLW1 was a major kernel weight QTL identified in the Nanda2419 × Wangshuibai population. We showed that introduction of the Nanda2419 allele into elite cultivar Wenmai6 resulted in longer kernels as well as higher kernel weight, without affecting other traits such as spike number per plant, plant height, spike length, spikelet number per spike, and kernel number per spike. KLW1 was dominant in conditioning higher kernel weight and functioned mainly through affecting kernel length. Using F2 plants derived from KLW1 NIL, a high-density genetic map covering the QTL was constructed. KLW1 was consequently confined to the 0.6 cM Xwgrc4219-Xwgrc4067 interval by evaluating the recombinant lines in three field trials. KLW1 is complementary to KT1, the QTL on chromosome 5A of Nanda2419 for thicker and heavier kernels, in producing larger kernels with higher commercial value, augmenting its usefulness in wheat breeding.
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Affiliation(s)
- Yang Yang
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhongxin Kong
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Quan Xie
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Haiyan Jia
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Wenshuo Huang
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Liwei Zhang
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Ruiru Cheng
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zibo Yang
- Huaiyin Institute of Agriculture Sciences of Xuhuai Region in Jiangsu, Huai'an, China
| | - Xiaolei Qi
- Tai'an Academy of Agricultural Sciences, Tai'an, China
| | - Guangde Lv
- Tai'an Academy of Agricultural Sciences, Tai'an, China
| | - Yong Zhang
- Huaiyin Institute of Agriculture Sciences of Xuhuai Region in Jiangsu, Huai'an, China
| | - Yixuan Wen
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Zhengqiang Ma
- Crop Genomics and Bioinformatics Center and National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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Zeng Z, Zhao D, Wang C, Yan X, Song J, Chen P, Lan C, Singh RP. QTL cluster analysis and marker development for kernel traits based on DArT markers in spring bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1072233. [PMID: 36844075 PMCID: PMC9951491 DOI: 10.3389/fpls.2023.1072233] [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: 10/17/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Genetic dissection of yield component traits including kernel characteristics is essential for the continuous improvement in wheat yield. In the present study, one recombinant inbred line (RIL) F6 population derived from a cross between Avocet and Chilero was used to evaluate the phenotypes of kernel traits of thousand-kernel weight (TKW), kernel length (KL), and kernel width (KW) in four environments at three experimental stations during the 2018-2020 wheat growing seasons. The high-density genetic linkage map was constructed with the diversity arrays technology (DArT) markers and the inclusive composite interval mapping (ICIM) method to identify the quantitative trait loci (QTLs) for TKW, KL, and KW. A total of 48 QTLs for three traits were identified in the RIL population on the 21 chromosomes besides 2A, 4D, and 5B, accounting for 3.00%-33.85% of the phenotypic variances. Based on the physical positions of each QTL, nine stable QTL clusters were identified in the RILs, and among these QTL clusters, TaTKW-1A was tightly linked to the DArT marker interval 3950546-1213099, explaining 10.31%-33.85% of the phenotypic variances. A total of 347 high-confidence genes were identified in a 34.74-Mb physical interval. TraesCS1A02G045300 and TraesCS1A02G058400 were among the putative candidate genes associated with kernel traits, and they were expressed during grain development. Moreover, we also developed high-throughput kompetitive allele-specific PCR (KASP) markers of TaTKW-1A, validated in a natural population of 114 wheat varieties. The study provides a basis for cloning the functional genes underlying the QTL for kernel traits and a practical and accurate marker for molecular breeding.
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Affiliation(s)
- Zhankui Zeng
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Dehui Zhao
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Chunping Wang
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Xuefang Yan
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Junqiao Song
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Peng Chen
- College of Agronomy, Henan University of Science and Technology, Luoyang, Henan, China
- The Shennong Laboratory, Zhengzhou, Henan, China
| | - Caixia Lan
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ravi P. Singh
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), Mexico, Mexico
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7
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Liu H, Shi Z, Ma F, Xu Y, Han G, Zhang J, Liu D, An D. Identification and validation of plant height, spike length and spike compactness loci in common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:568. [PMID: 36471256 PMCID: PMC9724413 DOI: 10.1186/s12870-022-03968-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Plant height (PH), spike length (SL) and spike compactness (SCN) are important agronomic traits in wheat due to their strong correlations with lodging and yield. Thus, dissection of their genetic basis is essential for the improvement of plant architecture and yield potential in wheat breeding. The objective of this study was to map quantitative trait loci (QTL) for PH, SL and SCN in a recombinant inbred line (RIL) population derived from the cross 'PuBing3228 × Gao8901' (PG-RIL) and to evaluate the potential values of these QTL to improve yield. RESULTS In the current study, Five, six and ten stable QTL for PH, SL, and SCN, respectively, were identified in at least two individual environments. Five major QTL QPh.cas-5A.3, QPh.cas-6A, QSl.cas-6B.2, QScn.cas-2B.2 and QScn.cas-6B explained 5.58-25.68% of the phenotypic variation. Notably, two, three and three novel stable QTL for PH, SL and SCN were identified in this study, which could provide further insights into the genetic factors that shape PH and spike morphology in wheat. Conditional QTL analysis revealed that QTL for SCN were mainly affected by SL. Moreover, a Kompetitive Allele Specific PCR (KASP) marker tightly linked to stable major QTL QPh.cas-5A.3 was developed and verified using the PG-RIL population and a natural population. CONCLUSIONS Twenty-one stable QTL related to PH, SL, and SCN were identified. These stable QTL and the user-friendly marker KASP8750 will facilitate future studies involving positional cloning and marker-assisted selection in breeding.
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Affiliation(s)
- Hong Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Zhipeng Shi
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Feifei Ma
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Yunfeng Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Guohao Han
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China
| | - Jinpeng Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071000, Hebei, China.
| | - Diaoguo An
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, 050022, China.
- The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
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Song J, Xu D, Dong Y, Li F, Bian Y, Li L, Luo X, Fei S, Li L, Zhao C, Zhang Y, Xia X, Ni Z, He Z, Cao S. Fine mapping and characterization of a major QTL for grain weight on wheat chromosome arm 5DL. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3237-3246. [PMID: 35904627 DOI: 10.1007/s00122-022-04182-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
We fine mapped QTL QTKW.caas-5DL for thousand kernel weight in wheat, predicted candidate genes and developed a breeding-applicable marker. Thousand kernel weight (TKW) is an important yield component trait in wheat, and identification of the underlying genetic loci is helpful for yield improvement. We previously identified a stable quantitative trait locus (QTL) QTKW.caas-5DL for TKW in a Doumai/Shi4185 recombinant inbred line (RIL) population. Here we performed fine mapping of QTKW.caas-5DL using secondary populations derived from 15 heterozygous recombinants and delimited the QTL to an approximate 3.9 Mb physical interval from 409.9 to 413.8 Mb according to the Chinese Spring (CS) reference genome. Analysis of genomic synteny showed that annotated genes in the physical interval had high collinearity among CS and eight other wheat genomes. Seven genes with sequence variation and/or differential expression between parents were predicted as candidates for QTKW.caas-5DL based on whole-genome resequencing and transcriptome assays. A kompetitive allele-specific PCR (KASP) marker for QTKW.caas-5DL was developed, and genotyping confirmed a significant association with TKW but not with other yield component traits in a panel of elite wheat cultivars. The superior allele of QTKW.caas-5DL was frequent in a panel of cultivars, suggesting that it had undergone positive selection. These findings not only lay a foundation for map-based cloning of QTKW.caas-5DL but also provide an efficient tool for marker-assisted selection.
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Affiliation(s)
- Jie Song
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100094, China
| | - Dengan Xu
- Shandong Province Key Laboratory of Dryland Farming Technology, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Yan Dong
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Faji Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, 202 Gongye North Road, Jinan, 250100, Shandong, China
| | - Yingjie Bian
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lingli Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xumei Luo
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shuaipeng Fei
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lei Li
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Cong Zhao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhongfu Ni
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100094, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Miao Y, Jing F, Ma J, Liu Y, Zhang P, Chen T, Che Z, Yang D. Major Genomic Regions for Wheat Grain Weight as Revealed by QTL Linkage Mapping and Meta-Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:802310. [PMID: 35222467 PMCID: PMC8866663 DOI: 10.3389/fpls.2022.802310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/06/2022] [Indexed: 05/21/2023]
Abstract
Grain weight is a key determinant for grain yield potential in wheat, which is highly governed by a type of quantitative genetic basis. The identification of major quantitative trait locus (QTL) and functional genes are urgently required for molecular improvements in wheat grain yield. In this study, major genomic regions and putative candidate genes for thousand grain weight (TGW) were revealed by integrative approaches with QTL linkage mapping, meta-analysis and transcriptome evaluation. Forty-five TGW QTLs were detected using a set of recombinant inbred lines, explaining 1.76-12.87% of the phenotypic variation. Of these, ten stable QTLs were identified across more than four environments. Meta-QTL (MQTL) analysis were performed on 394 initial TGW QTLs available from previous studies and the present study, where 274 loci were finally refined into 67 MQTLs. The average confidence interval of these MQTLs was 3.73-fold less than that of initial QTLs. A total of 134 putative candidate genes were mined within MQTL regions by combined analysis of transcriptomic and omics data. Some key putative candidate genes similar to those reported early for grain development and grain weight formation were further discussed. This finding will provide a better understanding of the genetic determinants of TGW and will be useful for marker-assisted selection of high yield in wheat breeding.
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Affiliation(s)
- Yongping Miao
- State Key Laboratory of Aridland Crop Science, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Gansu, China
| | - Fanli Jing
- State Key Laboratory of Aridland Crop Science, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Gansu, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Gansu, China
| | - Yuan Liu
- State Key Laboratory of Aridland Crop Science, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Gansu, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Gansu, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Gansu, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Gansu, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Gansu, China
- *Correspondence: Delong Yang,
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