1
|
Liu Y, Yu R, Shen L, Sun M, Peng Y, Zeng Q, Shen K, Yu X, Wu H, Ye B, Wang Z, Sun Z, Liu D, Sun X, Zhang Z, Dong J, Dong J, Han D, He Z, Hao Y, Wu J, Guo Z. Genomic insights into the modifications of spike morphology traits during wheat breeding. PLANT, CELL & ENVIRONMENT 2024. [PMID: 39205629 DOI: 10.1111/pce.15117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/04/2024]
Abstract
Over the past century, environmental changes have significantly impacted wheat spike morphology, crucial for adaptation and grain yield. However, the changes in wheat spike modifications during this period remain largely unknown. This study examines 16 spike morphology traits in 830 accessions released from 1900 to 2020. It finds that spike weight, grain number per spike (GN), and thousand kernel weight have significantly increased, while spike length has no significant change. The increase in fertile spikelets is due to fewer degenerated spikelets, resulting in a higher GN. Genome-wide association studies identified 49,994 significant SNPs, grouped into 293 genomic regions. The accumulation of favorable alleles in these genomic regions indicates the genetic basis for modification in spike morphology traits. Genetic network analysis of these genomic regions reveals the genetic basis for phenotypic correlations among spike morphology traits. The haplotypes of the identified genomic regions display obvious geographical differentiation in global accessions and environmental adaptation over the past 120 years. In summary, we reveal the genetic basis of adaptive evolution and the interactions of spike morphology, offering valuable resources for the genetic improvement of spike morphology to enhance environmental adaptation.
Collapse
Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Rui Yu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
| | - Mengjing Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yanchun Peng
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiweng Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Danning Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohui Sun
- Yantai Academy of Agricultural Sciences, Yantai, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jiayu Dong
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jing Dong
- Key Laboratory of Crop Molecular Breeding, Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Northwest A&F University, Yangling, Shaanxi, China
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
2
|
Niu J, Wang W, Wang Z, Chen Z, Zhang X, Qin Z, Miao L, Yang Z, Xie C, Xin M, Peng H, Yao Y, Liu J, Ni Z, Sun Q, Guo W. Tagging large CNV blocks in wheat boosts digitalization of germplasm resources by ultra-low-coverage sequencing. Genome Biol 2024; 25:171. [PMID: 38951917 PMCID: PMC11218387 DOI: 10.1186/s13059-024-03315-6] [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: 01/31/2024] [Accepted: 06/18/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND The massive structural variations and frequent introgression highly contribute to the genetic diversity of wheat, while the huge and complex genome of polyploid wheat hinders efficient genotyping of abundant varieties towards accurate identification, management, and exploitation of germplasm resources. RESULTS We develop a novel workflow that identifies 1240 high-quality large copy number variation blocks (CNVb) in wheat at the pan-genome level, demonstrating that CNVb can serve as an ideal DNA fingerprinting marker for discriminating massive varieties, with the accuracy validated by PCR assay. We then construct a digitalized genotyping CNVb map across 1599 global wheat accessions. Key CNVb markers are linked with trait-associated introgressions, such as the 1RS·1BL translocation and 2NvS translocation, and the beneficial alleles, such as the end-use quality allele Glu-D1d (Dx5 + Dy10) and the semi-dwarf r-e-z allele. Furthermore, we demonstrate that these tagged CNVb markers promote a stable and cost-effective strategy for evaluating wheat germplasm resources with ultra-low-coverage sequencing data, competing with SNP array for applications such as evaluating new varieties, efficient management of collections in gene banks, and describing wheat germplasm resources in a digitalized manner. We also develop a user-friendly interactive platform, WheatCNVb ( http://wheat.cau.edu.cn/WheatCNVb/ ), for exploring the CNVb profiles over ever-increasing wheat accessions, and also propose a QR-code-like representation of individual digital CNVb fingerprint. This platform also allows uploading new CNVb profiles for comparison with stored varieties. CONCLUSIONS The CNVb-based approach provides a low-cost and high-throughput genotyping strategy for enabling digitalized wheat germplasm management and modern breeding with precise and practical decision-making.
Collapse
Affiliation(s)
- Jianxia Niu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
- Sanya Institute of China Agricultural University, Sanya, 572025, China
| | - Zhe Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Xiaoyu Zhang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhen Qin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
3
|
Zhao Y, Dong Z, Miao J, Liu Q, Ma C, Tian X, He J, Bi H, Yao W, Li T, Gill HS, Zhang Z, Cao A, Liu B, Li H, Sehgal SK, Liu W. Pm57 from Aegilops searsii encodes a tandem kinase protein and confers wheat powdery mildew resistance. Nat Commun 2024; 15:4796. [PMID: 38839783 PMCID: PMC11153570 DOI: 10.1038/s41467-024-49257-2] [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: 04/21/2023] [Accepted: 05/29/2024] [Indexed: 06/07/2024] Open
Abstract
Powdery mildew is a devastating disease that affects wheat yield and quality. Wheat wild relatives represent valuable sources of disease resistance genes. Cloning and characterization of these genes will facilitate their incorporation into wheat breeding programs. Here, we report the cloning of Pm57, a wheat powdery mildew resistance gene from Aegilops searsii. It encodes a tandem kinase protein with putative kinase-pseudokinase domains followed by a von Willebrand factor A domain (WTK-vWA), being ortholog of Lr9 that mediates wheat leaf rust resistance. The resistance function of Pm57 is validated via independent mutants, gene silencing, and transgenic assays. Stable Pm57 transgenic wheat lines and introgression lines exhibit high levels of all-stage resistance to diverse isolates of the Bgt fungus, and no negative impacts on agronomic parameters are observed in our experimental set-up. Our findings highlight the emerging role of kinase fusion proteins in plant disease resistance and provide a valuable gene for wheat breeding.
Collapse
Affiliation(s)
- Yue Zhao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Zhenjie Dong
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, China
| | - Jingnan Miao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qianwen Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Chao Ma
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xiubin Tian
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Jinqiu He
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Huihui Bi
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Wen Yao
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Tao Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China
| | - Harsimardeep S Gill
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Aizhong Cao
- College of Agronomy, Nanjing Agricultural University, Nanjing, 210000, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Huanhuan Li
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD, 57007, USA.
| | - Wenxuan Liu
- State Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002, China.
| |
Collapse
|
4
|
Hu X, Yasir M, Zhuo Y, Cai Y, Ren X, Rong J. Genomic insights into glume pubescence in durum wheat: GWAS and haplotype analysis implicates TdELD1-1A as a candidate gene. Gene 2024; 909:148309. [PMID: 38417687 DOI: 10.1016/j.gene.2024.148309] [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: 09/21/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Glume pubescence is an important morphological trait for the characterization of wheat cultivars. It shows tolerance to biotic and abiotic stresses to some extent. Hg1 (formerly named Hg) locus on chromosome 1AS controls glume pubescence in wheat. Its genetic analysis, fine-mapping and candidate gene analysis have been widely studied recently, however, the cloning of Hg1 has not yet been reported. Here, we conducted a GWAS between a dense panel of 171,103 SNPs and glume pubescence (Gp) in a durum wheat population of 145 lines, and further analyzed the candidate genes of Hg1 combined with the gene expression, functional annotation, and haplotype analysis. As a results, TRITD0Uv1G104670 (TdELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was detected as the most promising candidate gene of Hg1 for glume pubescence in durum wheat. Our findings not only contribute to a deeper understanding of its cloning and functional validation but also underscore the significance of accurate genome sequences and annotations. Additionally, our study highlights the relevance of unanchored sequences in chrUn and the application of bioinformatics analysis for gene discovery in durum wheat.
Collapse
Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Yujie Zhuo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Yijing Cai
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
| |
Collapse
|
5
|
Leuenberger J, Sharma SK, McLean K, Pellé R, Bérard A, Lesage ML, Porhel D, Dantec MA, Chauvin JE, Bryan GJ, Pilet-Nayel ML, Kerlan MC, Esnault F. A genomic dataset integrating genotyping-by-sequencing, SolCAP array and PCR marker data on tetraploid potato advanced breeding lines. FRONTIERS IN PLANT SCIENCE 2024; 15:1384401. [PMID: 38828224 PMCID: PMC11141163 DOI: 10.3389/fpls.2024.1384401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 04/17/2024] [Indexed: 06/05/2024]
Affiliation(s)
- Julien Leuenberger
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
- Association des Créateurs de Variétés Nouvelle de Pomme de Terre (ACVNPT), Hanvec, France
| | - Sanjeev Kumar Sharma
- Cell & Molecular Science Department, The James Hutton Institute, Dundee, United Kingdom
| | - Karen McLean
- Cell & Molecular Science Department, The James Hutton Institute, Dundee, United Kingdom
| | - Roland Pellé
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | | | - Marie-Laure Lesage
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Danièle Porhel
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Marie-Ange Dantec
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Jean-Eric Chauvin
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Glenn J. Bryan
- Cell & Molecular Science Department, The James Hutton Institute, Dundee, United Kingdom
| | - Marie-Laure Pilet-Nayel
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Marie-Claire Kerlan
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| | - Florence Esnault
- Institut de Génétique, Environnement et Protection des Plantes (IGEPP), INRAE, Institut Agro, Univ Rennes, Ploudaniel, France
| |
Collapse
|
6
|
Wang Y, Wang Z, Chen Y, Lan T, Wang X, Liu G, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Guo W, Peng H. Genomic insights into the origin and evolution of spelt (Triticum spelta L.) as a valuable gene pool for modern wheat breeding. PLANT COMMUNICATIONS 2024; 5:100883. [PMID: 38491771 PMCID: PMC11121738 DOI: 10.1016/j.xplc.2024.100883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/22/2023] [Accepted: 03/13/2024] [Indexed: 03/18/2024]
Abstract
Spelt (Triticum aestivum ssp. spelta) is an important wheat subspecies mainly cultivated in Europe before the 20th century that has contributed to modern wheat breeding as a valuable genetic resource. However, relatively little is known about the origins and maintenance of spelt populations. Here, using resequencing data from 416 worldwide wheat accessions, including representative spelt wheat, we demonstrate that European spelt emerged when primitive hexaploid wheat spread to the west and hybridized with pre-settled domesticated emmer, the putative maternal donor. Genomic introgression regions from domesticated emmer confer spelt's primitive morphological characters used for species taxonomy, such as tenacious glumes and later flowering. We propose a haplotype-based "spelt index" to identify spelt-type wheat varieties and to quantify utilization of the spelt gene pool in modern wheat cultivars. This study reveals the genetic basis for the establishment of the spelt wheat subspecies in a specific ecological niche and the vital role of the spelt gene pool as a unique germplasm resource in modern wheat breeding.
Collapse
Affiliation(s)
- Yongfa Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Sanya Institute of China Agricultural University, Sanya 572025, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Tianyu Lan
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China; Institute for Plant Genetics, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Xiaobo Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Gang Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
7
|
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.
Collapse
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.)
| |
Collapse
|
8
|
Alam O, Purugganan MD. Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements. THE PLANT CELL 2024; 36:1227-1241. [PMID: 38243576 PMCID: PMC11062453 DOI: 10.1093/plcell/koae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 01/21/2024]
Abstract
Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops such as rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops such as rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits such as shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates such as resource acquisition rates and interactions with other organisms such as root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.
Collapse
Affiliation(s)
- Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
- Institute for the Study of the Ancient World, New York University, New York, NY, 10028, USA
| |
Collapse
|
9
|
Ma PF, Liu YL, Guo C, Jin G, Guo ZH, Mao L, Yang YZ, Niu LZ, Wang YJ, Clark LG, Kellogg EA, Xu ZC, Ye XY, Liu JX, Zhou MY, Luo Y, Yang Y, Soltis DE, Bennetzen JL, Soltis PS, Li DZ. Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance. Nat Genet 2024; 56:710-720. [PMID: 38491323 PMCID: PMC11018529 DOI: 10.1038/s41588-024-01683-0] [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: 03/08/2023] [Accepted: 02/08/2024] [Indexed: 03/18/2024]
Abstract
Polyploidy (genome duplication) is a pivotal force in evolution. However, the interactions between parental genomes in a polyploid nucleus, frequently involving subgenome dominance, are poorly understood. Here we showcase analyses of a bamboo system (Poaceae: Bambusoideae) comprising a series of lineages from diploid (herbaceous) to tetraploid and hexaploid (woody), with 11 chromosome-level de novo genome assemblies and 476 transcriptome samples. We find that woody bamboo subgenomes exhibit stunning karyotype stability, with parallel subgenome dominance in the two tetraploid clades and a gradual shift of dominance in the hexaploid clade. Allopolyploidization and subgenome dominance have shaped the evolution of tree-like lignified culms, rapid growth and synchronous flowering characteristic of woody bamboos as large grasses. Our work provides insights into genome dominance in a remarkable polyploid system, including its dependence on genomic context and its ability to switch which subgenomes are dominant over evolutionary time.
Collapse
Affiliation(s)
- Peng-Fei Ma
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yun-Long Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Cen Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Guihua Jin
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhen-Hua Guo
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ling Mao
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yi-Zhou Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Liang-Zhong Niu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yu-Jiao Wang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Lynn G Clark
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 345 Bessey, Ames, IA, USA
| | | | - Zu-Chang Xu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Xia-Ying Ye
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jing-Xia Liu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Meng-Yuan Zhou
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yan Luo
- Center for Integrative Conservation & Yunnan Key Laboratory for the Conservation of Tropical Rainforests and Asian Elephants, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, China
| | - Yang Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
- Department of Biology, University of Florida, Gainesville, FL, USA
| | | | - Pamela S Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, FL, USA
| | - De-Zhu Li
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China.
- Key Laboratory for Plant Diversity and Biogeography in East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China.
| |
Collapse
|
10
|
Coombes B, Lux T, Akhunov E, Hall A. Introgressions lead to reference bias in wheat RNA-seq analysis. BMC Biol 2024; 22:56. [PMID: 38454464 PMCID: PMC10921782 DOI: 10.1186/s12915-024-01853-w] [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: 10/20/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND RNA-seq is a fundamental technique in genomics, yet reference bias, where transcripts derived from non-reference alleles are quantified less accurately, can undermine the accuracy of RNA-seq quantification and thus the conclusions made downstream. Reference bias in RNA-seq analysis has yet to be explored in complex polyploid genomes despite evidence that they are often a complex mosaic of wild relative introgressions, which introduce blocks of highly divergent genes. RESULTS Here we use hexaploid wheat as a model complex polyploid, using both simulated and experimental data to show that RNA-seq alignment in wheat suffers from widespread reference bias which is largely driven by divergent introgressed genes. This leads to underestimation of gene expression and incorrect assessment of homoeologue expression balance. By incorporating gene models from ten wheat genome assemblies into a pantranscriptome reference, we present a novel method to reduce reference bias, which can be readily scaled to capture more variation as new genome and transcriptome data becomes available. CONCLUSIONS This study shows that the presence of introgressions can lead to reference bias in wheat RNA-seq analysis. Caution should be exercised by researchers using non-sample reference genomes for RNA-seq alignment and novel methods, such as the one presented here, should be considered.
Collapse
Affiliation(s)
| | - Thomas Lux
- Plant Genome and Systems Biology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Anthony Hall
- Earlham Institute, Norwich, Norfolk, NR4 7UZ, UK.
| |
Collapse
|
11
|
Chen Y, Wang W, Yang Z, Peng H, Ni Z, Sun Q, Guo W. Innovative computational tools provide new insights into the polyploid wheat genome. ABIOTECH 2024; 5:52-70. [PMID: 38576428 PMCID: PMC10987449 DOI: 10.1007/s42994-023-00131-7] [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: 09/13/2023] [Accepted: 12/14/2023] [Indexed: 04/06/2024]
Abstract
Bread wheat (Triticum aestivum) is an important crop and serves as a significant source of protein and calories for humans, worldwide. Nevertheless, its large and allopolyploid genome poses constraints on genetic improvement. The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging. Recently, we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome. Here, we summarize the methodological innovations and applications of these tools and databases. A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits. Furthermore, we outline future perspectives on new advanced tools and databases, taking into consideration the unique features of bread wheat, to accelerate genomic-assisted wheat breeding.
Collapse
Affiliation(s)
- Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhengzhao Yang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
12
|
Bi C, Wei C, Li J, Wen S, Zhao H, Yu J, Shi X, Zhang Y, Liu Q, Zhang Y, Li B, You M. A novel variation of TaGW2-6B increases grain weight without penalty in grain protein content in wheat ( Triticum aestivum L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2024; 44:15. [PMID: 38362529 PMCID: PMC10864231 DOI: 10.1007/s11032-024-01455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024]
Abstract
Yield and quality are two crucial breeding objects of wheat therein grain weight and grain protein content (GPC) are two key relevant factors correspondingly. Investigations of their genetic mechanisms represent special significance for breeding. In this study, 199 F2 plants and corresponding F2:3 families derived from Nongda3753 (ND3753) and its EMS-generated mutant 564 (M564) were used to investigate the genetic basis of larger grain and higher GPC of M564. QTL analysis identified a total of 33 environmentally stable QTLs related to thousand grain weight (TGW), grain area (GA), grain circle (GC), grain length (GL), grain width (GW), and GPC on chromosomes 1B, 2A, 2B, 4D, 6B, and 7D, respectively, among which QGw.cau-6B.1, QTgw.cau-6B.1, QGa.cau-6B.1, and QGc.cau-6B.1 shared overlap confidence interval on chromosome 6B. This interval contained the TaGW2 gene playing the same role as the QTLs, so TaGW2-6B was cloned and sequenced. Sequence alignment revealed two G/A SNPs between two parents, among which the SNP in the seventh exon led to a premature termination in M564. A KASP marker was developed based on the SNP, and single-marker analysis on biparental populations showed that the mutant allele could significantly increase GW and TGW, but had no effect on GPC. Distribution detection of the mutant allele through KASP marker genotyping and sequence alignment against databases ascertained that no materials harbored this allele within natural populations. This allele was subsequently introduced into three different varieties through molecular marker-assisted backcrossing, and it was revealed that the allele had a significant effect on simultaneously increasing GW, TGW, and even GPC in all of three backgrounds. Summing up the above, it could be concluded that a novel elite allele of TaGW2-6B was artificially created and might play an important role in wheat breeding for high yield and quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-024-01455-y.
Collapse
Affiliation(s)
- Chan Bi
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Chaoxiong Wei
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jinghui Li
- Wheat Center, Henan Institute of Science and Technology, Henan Provincial Key Laboratory of Hybrid Wheat, Xinxiang, 453003 China
| | - Shaozhe Wen
- Department of Landscape and Garden, Yangzhou Polytechnic College, Yangzhou, 225009 China
| | - Huanhuan Zhao
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Jiazheng Yu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Xintian Shi
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yuan Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Qiaofeng Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Yufeng Zhang
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Baoyun Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| | - Mingshan You
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Ministry of Education, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193 China
| |
Collapse
|
13
|
Jia J, Zhao G, Li D, Wang K, Kong C, Deng P, Yan X, Zhang X, Lu Z, Xu S, Jiao Y, Chong K, Liu X, Cui D, Li G, Zhang Y, Du C, Wu L, Li T, Yan D, Zhan K, Chen F, Wang Z, Zhang L, Kong X, Ru Z, Wang D, Gao L. Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement. MOLECULAR PLANT 2023; 16:1893-1910. [PMID: 37897037 DOI: 10.1016/j.molp.2023.10.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 07/12/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
Despite recent progress in crop genomics studies, the genomic changes brought about by modern breeding selection are still poorly understood, thus hampering genomics-assisted breeding, especially in polyploid crops with compound genomes such as common wheat (Triticum aestivum). In this work, we constructed genome resources for the modern elite common wheat variety Aikang 58 (AK58). Comparative genomics between AK58 and the landrace cultivar Chinese Spring (CS) shed light on genomic changes that occurred through recent varietal improvement. We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study (HGWAS) approach, which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci. A total of 123 major HGWAS loci were detected using a genetic population derived from AK58 and CS. Elite homoeologous haplotypes (HHs), formed by combinations of subgenomic homoeologs of the associated loci, were found in both parents and progeny, and many could substantially improve wheat yield and related traits. We built a website where users can download genome assembly sequence and annotation data for AK58, perform blast analysis, and run JBrowse. Our work enriches genome resources for wheat, provides new insights into genomic changes during modern wheat improvement, and suggests that efficient mining of elite HHs can make a substantial contribution to genomics-assisted breeding in common wheat and other polyploid crops.
Collapse
Affiliation(s)
- Jizeng Jia
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Wang
- Xi'An Shansheng Biosciences Co., Ltd., Xi'an 710000, China
| | - Chuizheng Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Pingchuan Deng
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 612100, China
| | - Xueqing Yan
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xueyong Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shujuan Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Yuannian Jiao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Chong
- University of Chinese Academy of Sciences, Beijing 100049, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dangqun Cui
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Guangwei Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yijing Zhang
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chunguang Du
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Liang Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, China; Hainan Yazhou Bay Seed Laboratory, Hainan Institute of Zhejiang University, Sanya, Hainan 562000, China
| | - Tianbao Li
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China; State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dong Yan
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kehui Zhan
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Feng Chen
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Zhiyong Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhengang Ru
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Daowen Wang
- College of Agronomy, Collaborative Innovation Center of Henan Grain Crops, State Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Lifeng Gao
- State Key Laboratory of Crop Gene Resources and Breeding, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
14
|
Niu J, Ma S, Zheng S, Zhang C, Lu Y, Si Y, Tian S, Shi X, Liu X, Naeem MK, Sun H, Hu Y, Wu H, Cui Y, Chen C, Long W, Zhang Y, Gu M, Cui M, Lu Q, Zhou W, Peng J, Akhunov E, He F, Zhao S, Ling HQ. Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States. THE PLANT CELL 2023; 35:4199-4216. [PMID: 37647532 PMCID: PMC10689146 DOI: 10.1093/plcell/koad229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/25/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023]
Abstract
Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.
Collapse
Affiliation(s)
- Jianqing Niu
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shengwei Ma
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shusong Zheng
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Yaru Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaoqi Si
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuiquan Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoli Shi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaolin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Muhammad Kashif Naeem
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Hu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Huilan Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunlin Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenbo Long
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yue Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengjun Gu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Man Cui
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qiao Lu
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenjuan Zhou
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Junhua Peng
- Huazhi Bio-tech Company Ltd., Changsha, Hunan 410125, China
| | - Eduard Akhunov
- Wheat Genetic Resources Center, Kansas State University, Manhattan, KS 66506, USA
| | - Fei He
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
| | - Hong-Qing Ling
- Hainan Yazhou Bay Seed Laboratory, Hainan, Sanya 572024, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
15
|
Bian Y, Li L, Tian X, Xu D, Sun M, Li F, Xie L, Liu S, Liu B, Xia X, He Z, Cao S. Rht12b, a widely used ancient allele of TaGA2oxA13, reduces plant height and enhances yield potential in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:253. [PMID: 37989964 DOI: 10.1007/s00122-023-04502-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023]
Abstract
KEY MESSAGE We identified a new wheat dwarfing allele Rht12b conferring reduced height and higher grain yield, pinpointed its causal variations, developed a breeding-applicable marker, and traced its origin and worldwide distribution. Plant height control is essential to optimize lodging resistance and yield gain in crops. RHT12 is a reduced height (Rht) locus that is identified in a mutationally induced dwarfing mutant and encodes a gibberellin 2-oxidase TaGA2oxA13. However, the artificial dwarfing allele is not used in wheat breeding due to excessive height reduction. Here, we confirmed a stable Rht locus, overlapping with RHT12, in a panel of wheat cultivars and its dwarfing allele reduced plant height by 5.4-8.2 cm, equivalent to Rht12b, a new allele of RHT12. We validated the effect of Rht12b on plant height in a bi-parent mapping population. Importantly, wheat cultivars carrying Rht12b had higher grain yield than those with the contrasting Rht12a allele. Rht12b conferred higher expression level of TaGA2oxA13. Transient activation assays defined SNP-390(C/A) in the promoter of TaGA2oxA13 as the causal variation. An efficient kompetitive allele-specific PCR marker was developed to diagnose Rht12b. Conjoint analysis showed that Rht12b plus the widely used Rht-D1b, Rht8 and Rht24b was the predominant Rht combination and conferred a moderate plant height in tested wheat cultivars. Evolutionary tracking uncovered that RHT12 locus arose from a tandem duplication event with Rht12b firstly appearing in wild emmer. The frequency of Rht12b was approximately 70% (700/1005) in a worldwide wheat panel and comparable to or higher than those of other widely used Rht genes, suggesting it had been subjected to positive selection. These findings not only identify a valuable Rht gene for wheat improvement but also develop a functionally diagnostic tool for marker-assisted breeding.
Collapse
Affiliation(s)
- Yingjie Bian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Lingli Li
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xiuling Tian
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dengan Xu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Mengjing Sun
- National Wheat Improvement Center, Institute of Crop Sciences, 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
| | - Lina Xie
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Siyang Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Bingyan Liu
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- International Maize and Wheat Improvement Center China Office, c/o Chinese Academy Agricultural Sciences, Beijing, 100081, China.
| | - Shuanghe Cao
- National Wheat Improvement Center, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| |
Collapse
|
16
|
Zhou X, Zhao Y, Ni P, Ni Z, Sun Q, Zong Y. CRISPR-mediated acceleration of wheat improvement: advances and perspectives. J Genet Genomics 2023; 50:815-834. [PMID: 37741566 DOI: 10.1016/j.jgg.2023.09.007] [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: 08/18/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Common wheat (Triticum aestivum) is one of the most widely cultivated and consumed crops globally. In the face of limited arable land and climate changes, it is a great challenge to maintain current and increase future wheat production. Enhancing agronomic traits in wheat by introducing mutations across all three homoeologous copies of each gene has proven to be a difficult task due to its large genome with high repetition. However, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease (Cas) genome editing technologies offer a powerful means of precisely manipulating the genomes of crop species, thereby opening up new possibilities for biotechnology and breeding. In this review, we first focus on the development and optimization of the current CRISPR-based genome editing tools in wheat, emphasizing recent breakthroughs in precise and multiplex genome editing. We then describe the general procedure of wheat genome editing and highlight different methods to deliver the genome editing reagents into wheat cells. Furthermore, we summarize the recent applications and advancements of CRISPR/Cas technologies for wheat improvement. Lastly, we discuss the remaining challenges specific to wheat genome editing and its future prospects.
Collapse
Affiliation(s)
- Ximeng Zhou
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Pei Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yuan Zong
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
17
|
Wang Z, Miao L, Chen Y, Peng H, Ni Z, Sun Q, Guo W. Deciphering the evolution and complexity of wheat germplasm from a genomic perspective. J Genet Genomics 2023; 50:846-860. [PMID: 37611848 DOI: 10.1016/j.jgg.2023.08.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/29/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023]
Abstract
Bread wheat provides an essential fraction of the daily calorific intake for humanity. Due to its huge and complex genome, progress in studying on the wheat genome is substantially trailed behind those of the other two major crops, rice and maize, for at least a decade. With rapid advances in genome assembling and reduced cost of high-throughput sequencing, emerging de novo genome assemblies of wheat and whole-genome sequencing data are leading to a paradigm shift in wheat research. Here, we review recent progress in dissecting the complex genome and germplasm evolution of wheat since the release of the first high-quality wheat genome. New insights have been gained in the evolution of wheat germplasm during domestication and modern breeding progress, genomic variations at multiple scales contributing to the diversity of wheat germplasm, and complex transcriptional and epigenetic regulations of functional genes in polyploid wheat. Genomics databases and bioinformatics tools meeting the urgent needs of wheat genomics research are also summarized. The ever-increasing omics data, along with advanced tools and well-structured databases, are expected to accelerate deciphering the germplasm and gene resources in wheat for future breeding advances.
Collapse
Affiliation(s)
- Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lingfeng Miao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yongming Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
18
|
Li M, Liu T, Cao R, Cao Q, Tong W, Song W. Evolution and Expression of the Expansin Genes in Emmer Wheat. Int J Mol Sci 2023; 24:14120. [PMID: 37762423 PMCID: PMC10531347 DOI: 10.3390/ijms241814120] [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: 07/12/2023] [Revised: 09/10/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Expansin proteins, a crucial class of intracellular proteins, are known to play a vital role in facilitating processes like cell wall relaxation and cell growth. Recent discoveries have revealed that expansin proteins also have significant functions in plant growth, development, and response to resistance. However, the expansin gene family, particularly in emmer wheat, has not been thoroughly studied, particularly in terms of evolution. In this study, we identified 63 TdEXPs and 49 TtEXPs from the latest genome versions of wild emmer wheat (WEW) and durum wheat (DW), respectively. The physicochemical properties of the encoded expansin proteins exhibited minimal differences, and the gene structures remained relatively conserved. Phylogenetic analysis categorized the proteins into three subfamilies, namely EXPA, EXPB, and EXLA, in addition to the EXLB subfamily. Furthermore, codon preference analysis revealed an increased usage frequency of the nucleotide "T" in expansin proteins throughout the evolution of WEW and DW. Collinearity analysis demonstrated higher orthology between the expansin proteins of WEW and DW, with a Ka/Ks ratio ranging from 0.4173 to 0.9494, indicating purifying selection during the evolution from WEW to DW. Haplotype analysis of the expansin gene family identified five genes in which certain haplotypes gradually became dominant over the course of evolution, enabling adaptation for survival and improvement. Expression pattern analysis indicated tissue-specific expression of expansin genes in emmer wheat, and some of these genes were quantified through qRT-PCR to assess their response to salt stress. These comprehensive findings present the first systematic analysis of the expansin protein gene family during the evolution from WEW to DW, providing a foundation for further understanding the functions and biological roles of expansin protein genes in emmer wheat.
Collapse
Affiliation(s)
| | | | | | | | - Wei Tong
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (M.L.); (T.L.); (R.C.); (Q.C.)
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Xianyang 712100, China; (M.L.); (T.L.); (R.C.); (Q.C.)
| |
Collapse
|
19
|
Ma H, Ding W, Chen Y, Zhou J, Chen W, Lan C, Mao H, Li Q, Yan W, Su H. Centromere Plasticity With Evolutionary Conservation and Divergence Uncovered by Wheat 10+ Genomes. Mol Biol Evol 2023; 40:msad176. [PMID: 37541261 PMCID: PMC10422864 DOI: 10.1093/molbev/msad176] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/26/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023] Open
Abstract
Centromeres (CEN) are the chromosomal regions that play a crucial role in maintaining genomic stability. The underlying highly repetitive DNA sequences can evolve quickly in most eukaryotes, and promote karyotype evolution. Despite their variability, it is not fully understood how these widely variable sequences ensure the homeostasis of centromere function. In this study, we investigated the genetics and epigenetics of CEN in a population of wheat lines from global breeding programs. We captured a high degree of sequences, positioning, and epigenetic variations in the large and complex wheat CEN. We found that most CENH3-associated repeats are Cereba element of retrotransposons and exhibit phylogenetic homogenization across different wheat lines, but the less-associated repeat sequences diverge on their own way in each wheat line, implying specific mechanisms for selecting certain repeat types as functional core CEN. Furthermore, we observed that CENH3 nucleosome structures display looser wrapping of DNA termini on complex centromeric repeats, including the repositioned CEN. We also found that strict CENH3 nucleosome positioning and intrinsic DNA features play a role in determining centromere identity among different lines. Specific non-B form DNAs were substantially associated with CENH3 nucleosomes for the repositioned centromeres. These findings suggest that multiple mechanisms were involved in the adaptation of CENH3 nucleosomes that can stabilize CEN. Ultimately, we proposed a remarkable epigenetic plasticity of centromere chromatin within the diverse genomic context, and the high robustness is crucial for maintaining centromere function and genome stability in wheat 10+ lines as a result of past breeding selections.
Collapse
Affiliation(s)
- Huan Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Wentao Ding
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Yiqian Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Jingwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Qiang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
| | - Handong Su
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| |
Collapse
|
20
|
Wu D, Xie L, Sun Y, Huang Y, Jia L, Dong C, Shen E, Ye CY, Qian Q, Fan L. A syntelog-based pan-genome provides insights into rice domestication and de-domestication. Genome Biol 2023; 24:179. [PMID: 37537691 PMCID: PMC10401782 DOI: 10.1186/s13059-023-03017-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/19/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Asian rice is one of the world's most widely cultivated crops. Large-scale resequencing analyses have been undertaken to explore the domestication and de-domestication genomic history of Asian rice, but the evolution of rice is still under debate. RESULTS Here, we construct a syntelog-based rice pan-genome by integrating and merging 74 high-accuracy genomes based on long-read sequencing, encompassing all ecotypes and taxa of Oryza sativa and Oryza rufipogon. Analyses of syntelog groups illustrate subspecies divergence in gene presence-and-absence and haplotype composition and identify massive genomic regions putatively introgressed from ancient Geng/japonica to ancient Xian/indica or its wild ancestor, including almost all well-known domestication genes and a 4.5-Mbp centromere-spanning block, supporting a single domestication event in main rice subspecies. Genomic comparisons between weedy and cultivated rice highlight the contribution from wild introgression to the emergence of de-domestication syndromes in weedy rice. CONCLUSIONS This work highlights the significance of inter-taxa introgression in shaping diversification and divergence in rice evolution and provides an exploratory attempt by utilizing the advantages of pan-genomes in evolutionary studies.
Collapse
Affiliation(s)
- Dongya Wu
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- Center for Evolutionary & Organismal Biology, Zhejiang University, Hangzhou, 310058, China
| | - Lingjuan Xie
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yanqing Sun
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Yujie Huang
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Lei Jia
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chenfeng Dong
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Hainan Institute of Zhejiang University, Sanya, 572025, China
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Chu-Yu Ye
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Longjiang Fan
- Hainan Institute of Zhejiang University, Sanya, 572025, China.
- Institute of Crop Science, Zhejiang University, Hangzhou, 310058, China.
| |
Collapse
|
21
|
Lev-Mirom Y, Distelfeld A. Where was wheat domesticated? NATURE PLANTS 2023; 9:1201-1202. [PMID: 37488266 DOI: 10.1038/s41477-023-01467-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 07/26/2023]
Affiliation(s)
- Yael Lev-Mirom
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences and the Institute of Evolution, University of Haifa, Haifa, Israel
| | - Assaf Distelfeld
- Department of Evolutionary and Environmental Biology, Faculty of Natural Sciences and the Institute of Evolution, University of Haifa, Haifa, Israel.
| |
Collapse
|
22
|
Gao Z, Bian J, Lu F, Jiao Y, He H. Triticeae crop genome biology: an endless frontier. FRONTIERS IN PLANT SCIENCE 2023; 14:1222681. [PMID: 37546276 PMCID: PMC10399237 DOI: 10.3389/fpls.2023.1222681] [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: 05/15/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023]
Abstract
Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.
Collapse
Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuling Jiao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| |
Collapse
|
23
|
Liu H, Si X, Wang Z, Cao L, Gao L, Zhou X, Wang W, Wang K, Jiao C, Zhuang L, Liu Y, Hou J, Li T, Hao C, Guo W, Liu J, Zhang X. TaTPP-7A positively feedback regulates grain filling and wheat grain yield through T6P-SnRK1 signalling pathway and sugar-ABA interaction. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1159-1175. [PMID: 36752567 DOI: 10.1111/pbi.14025] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 05/27/2023]
Abstract
Grain size and filling are two key determinants of grain thousand-kernel weight (TKW) and crop yield, therefore they have undergone strong selection since cereal was domesticated. Genetic dissection of the two traits will improve yield potential in crops. A quantitative trait locus significantly associated with wheat grain TKW was detected on chromosome 7AS flanked by a simple sequence repeat marker of Wmc17 in Chinese wheat 262 mini-core collection by genome-wide association study. Combined with the bulked segregant RNA-sequencing (BSR-seq) analysis of an F2 genetic segregation population with extremely different TKW traits, a candidate trehalose-6-phosphate phosphatase gene located at 135.0 Mb (CS V1.0), designated as TaTPP-7A, was identified. This gene was specifically expressed in developing grains and strongly influenced grain filling and size. Overexpression (OE) of TaTPP-7A in wheat enhanced grain TKW and wheat yield greatly. Detailed analysis revealed that OE of TaTPP-7A significantly increased the expression levels of starch synthesis- and senescence-related genes involved in abscisic acid (ABA) and ethylene pathways. Moreover, most of the sucrose metabolism and starch regulation-related genes were potentially regulated by SnRK1. In addition, TaTPP-7A is a crucial domestication- and breeding-targeted gene and it feedback regulates sucrose lysis, flux, and utilization in the grain endosperm mainly through the T6P-SnRK1 pathway and sugar-ABA interaction. Thus, we confirmed the T6P signalling pathway as the central regulatory system for sucrose allocation and source-sink interactions in wheat grains and propose that the trehalose pathway components have great potential to increase yields in cereal crops.
Collapse
Affiliation(s)
- Hongxia Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xuemei Si
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Zhenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Liangjing Cao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xiaolong Zhou
- Beijing Biomics Biotechnology Company limited, Beijing, China
| | - Wenxi Wang
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Ke Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chengzhi Jiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Lei Zhuang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yunchuan Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jian Hou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Tian Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chenyang Hao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Jun Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| |
Collapse
|
24
|
Dondup D, Yang Y, Xu D, Namgyal L, Wang Z, Shen X, Dorji T, kyi N, Drolma L, Gao L, Ga Z, Sang Z, Ga Z, Mu W, Zhuoma P, Taba X, Jiao G, Liao W, Tang Y, Zeng X, Luobu Z, Wu Y, Wang C, Zhang J, Qi Z, Guo W, Guo G. Genome diversity and highland-adaptative variation in Tibet barley landrace population of China. FRONTIERS IN PLANT SCIENCE 2023; 14:1189642. [PMID: 37235004 PMCID: PMC10206316 DOI: 10.3389/fpls.2023.1189642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023]
Abstract
Barley landraces accumulated variation in adapting to extreme highland environments during long-term domestication in Tibet, but little is known about their population structure and genomic selection traces. In this study, tGBS (tunable genotyping by sequencing) sequencing, molecular marker and phenotypic analyses were conducted on 1,308 highland and 58 inland barley landraces in China. The accessions were divided into six sub-populations and clearly distinguished most six-rowed, naked barley accessions (Qingke in Tibet) from inland barley. Genome-wide differentiation was observed in all five sub-populations of Qingke and inland barley accessions. High genetic differentiation in the pericentric regions of chromosomes 2H and 3H contributed to formation of five types of Qingke. Ten haplotypes of the pericentric regions of 2H, 3H, 6H and 7H were further identified as associated with ecological diversification of these sub-populations. There was genetic exchange between eastern and western Qingke but they shared the same progenitor. The identification of 20 inland barley types indicated multiple origins of Qingke in Tibet. The distribution of the five types of Qingke corresponded to specific environments. Two predominant highland-adaptative variations were identified for low temperature tolerance and grain color. Our results provide new insights into the origin, genome differentiation, population structure and highland adaptation in highland barley which will benefit both germplasm enhancement and breeding of naked barley.
Collapse
Affiliation(s)
- Dawa Dondup
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
- College of Plant Science, Tibet Agricultural and Husbandry University, Linzhi, China
| | - Yang Yang
- College of Life Sciences, Zaozhuang University, Zaozhuang, China
| | - Dongdong Xu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
- Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Lhundrup Namgyal
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Xia Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tsechoe Dorji
- Key Laboratory of Alpine Ecology and Biodiversity, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Tibetan Plateau Earth Science, Chinese Academy of Sciences, Beijing, China
| | - Nyima kyi
- Tibet Climate Center, Tibet Meteorological Bureau, Lhasa, China
| | - Lhakpa Drolma
- Tibet Institute of Plateau Atmospheric and Environmental Sciences, Tibet Meteorological Bureau, Lhasa, China
- Key Laboratory of Atmospheric Environment of Tibet Autonomous Region, Tibet Meteorological Bureau, Lhasa, China
| | - Liyun Gao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhuo Ga
- College of Plant Science, Tibet Agricultural and Husbandry University, Linzhi, China
| | - Zha Sang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhuo Ga
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Wang Mu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Pubu Zhuoma
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Xiongnu Taba
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Guocheng Jiao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Wenhua Liao
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yawei Tang
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Xingquan Zeng
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Zhaxi Luobu
- State Key Laboratory of Hulless Barley and Yak Germplasm Resources and Genetic Improvement, Research Institute of Agriculture, Tibet Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Yufeng Wu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| | - Zengjun Qi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing, China
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing, China
| |
Collapse
|
25
|
Ke W, Xing J, Chen Z, Zhao Y, Xu W, Tian L, Guo J, Xie X, Du D, Wang Z, Li Y, Xu J, Xin M, Guo W, Hu Z, Su Z, Liu J, Peng H, Yao Y, Sun Q, Ni Z. The TaTCP4/10-B1 cascade regulates awn elongation in wheat (Triticum aestivum L.). PLANT COMMUNICATIONS 2023:100590. [PMID: 36919240 PMCID: PMC10363512 DOI: 10.1016/j.xplc.2023.100590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Awns are important morphological markers for wheat and exert a strong physiological effect on wheat yield. The awn elongation suppressor B1 has recently been cloned through association and linkage analysis in wheat. However, the mechanism of awn inhibition centered around B1 remains to be clarified. Here, we identified an allelic variant in the coding region of B1 through analysis of re-sequencing data; this variant causes an amino acid substitution and premature termination, resulting in a long-awn phenotype. Transcriptome analysis indicated that B1 inhibited awn elongation by impeding cytokinin- and auxin-promoted cell division. Moreover, B1 directly repressed the expression of TaRAE2 and TaLks2, whose orthologs have been reported to promote awn development in rice or barley. More importantly, we found that TaTCP4 and TaTCP10 synergistically inhibited the expression of B1, and a G-to-A mutation in the B1 promoter attenuated its inhibition by TaTCP4/10. Taken together, our results reveal novel mechanisms of awn development and provide genetic resources for trait improvement in wheat.
Collapse
Affiliation(s)
- Wensheng Ke
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jiewen Xing
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaoyan Chen
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yidi Zhao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weiya Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Lulu Tian
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jinquan Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Xiaoming Xie
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Dejie Du
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yufeng Li
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jin Xu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhenqi Su
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
26
|
Zhao X, Guo Y, Kang L, Yin C, Bi A, Xu D, Zhang Z, Zhang J, Yang X, Xu J, Xu S, Song X, Zhang M, Li Y, Kear P, Wang J, Liu Z, Fu X, Lu F. Population genomics unravels the Holocene history of bread wheat and its relatives. NATURE PLANTS 2023; 9:403-419. [PMID: 36928772 DOI: 10.1038/s41477-023-01367-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 02/08/2023] [Indexed: 05/06/2023]
Abstract
Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.
Collapse
Affiliation(s)
- Xuebo Zhao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yafei Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lipeng Kang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Aoyue Bi
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Daxing Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhiliang Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jijin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaohan Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jun Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Song Xu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xinyue Song
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming, China
| | - Ming Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Philip Kear
- International Potato Center-China Center for Asia and the Pacific, Beijing, China
| | - Jing Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
27
|
Li C, Zhuang L, Li T, Hou J, Liu H, Jian C, Li H, Zhao J, Liu Y, Xi W, Hao P, Liu S, Si X, Wang X, Zhang X, Hao C. Conservatively transmitted alleles of key agronomic genes provide insights into the genetic basis of founder parents in bread wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2023; 23:100. [PMID: 36805674 PMCID: PMC9938602 DOI: 10.1186/s12870-023-04098-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Founder parents play extremely important roles in wheat breeding. Studies into the genetic basis of founder parents and the transmission rules of favorable alleles are of great significance in improving agronomically important traits in wheat. RESULTS Here, a total of 366 founder parents, widely grown cultivars, and derivatives of four representative founder parents were genotyped based on efficient kompetitive allele-specific PCR (KASP) markers in 87 agronomically important genes controlling yield, quality, adaptability, and stress resistance. Genetic composition analysis of founder parents and widely grown cultivars showed a consistently high frequency of favorable alleles for yield-related genes. This analysis further showed that other alleles favorable for resistance, strong gluten, dwarf size, and early heading date were also subject to selective pressure over time. By comparing the transmission of alleles from four representative founder parents to their derivatives during different breeding periods, it was found that the genetic composition of the representative founder parents was optimized as breeding progressed over time, with the number and types of favorable alleles carried gradually increasing and becoming enriched. There are still a large number of favorable alleles in wheat founder parents that have not been fully utilized in breeding selection. Eighty-seven agronomically important genes were used to construct an enrichment map that shows favorable alleles of four founder parents, providing an important theoretical foundation for future identification of candidate wheat founder parents. CONCLUSIONS These results reveal the genetic basis of founder parents and allele transmission for 87 agronomically important genes and shed light on breeding strategies for the next generation of elite founder parents in wheat.
Collapse
Affiliation(s)
- Chang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Lei Zhuang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Huifang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Jing Zhao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Yunchuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Wei Xi
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Pingan Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Shujuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xuemei Si
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xiaolu Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs/The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| |
Collapse
|
28
|
Broccanello C, Bellin D, DalCorso G, Furini A, Taranto F. Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change. FRONTIERS IN PLANT SCIENCE 2023; 14:1101271. [PMID: 36778704 PMCID: PMC9911883 DOI: 10.3389/fpls.2023.1101271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.
Collapse
Affiliation(s)
| | - Diana Bellin
- Department of Biotechnology, University of Verona, Verona, Italy
| | | | - Antonella Furini
- Department of Biotechnology, University of Verona, Verona, Italy
| | | |
Collapse
|
29
|
Zhao J, Zheng X, Qiao L, Yang C, Wu B, He Z, Tang Y, Li G, Yang Z, Zheng J, Qi Z. Genome-wide association study reveals structural chromosome variations with phenotypic effects in wheat (Triticum aestivum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1447-1461. [PMID: 36345647 DOI: 10.1111/tpj.16023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/26/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Structural chromosome variations (SCVs) are large-scale genomic variations that can be detected by fluorescence in situ hybridization (FISH). SCVs have played important roles in the genome evolution of wheat (Triticum aestivum L.), but little is known about their genetic effects. In this study, a total of 543 wheat accessions from the Chinese wheat mini-core collection and the Shanxi Province wheat collection were used for chromosome analysis using oligonucleotide probe multiplex FISH. A total of 139 SCVs including translocations, pericentric inversions, presence/absence variations (PAVs), and copy number variations (CNVs) in heterochromatin were identified at 230 loci. The distribution frequency of SCVs varied between ecological regions and between landraces and modern cultivars. Structural analysis using SCVs as markers clearly divided the landraces and modern cultivars into different groups. There are very clear instances illustrating alien introgression and wide application of foreign germplasms improved the chromosome diversity of Chinese modern wheat cultivars. A genome-wide association study (GWAS) identified 29 SCVs associated with 12 phenotypic traits, and five (RT4AS•4AL-1DS/1DL•1DS-4AL, Mg2A-3, Mr3B-10, Mr7B-13, and Mr4A-7) of them were further validated using a doubled haploid population and advanced sib-lines, implying the potential value of these SCVs. Importantly, the number of favored SCVs that were associated with agronomic trait improvement was significantly higher in modern cultivars compared to landraces, indicating positive selection in wheat breeding. This study demonstrates the significant effects of SCVs during wheat breeding and provides an efficient method of mining favored SCVs in wheat and other crops.
Collapse
Affiliation(s)
- Jiajia Zhao
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingwei Zheng
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Ling Qiao
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Chenkang Yang
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Bangbang Wu
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Ziming He
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yuqing Tang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangrong Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Zujun Yang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic and Technology of China, Chengdu, 611731, China
| | - Jun Zheng
- Institute of Wheat Research, State Key Laboratory of Sustainable Dryland Agriculture, Shanxi Agricultural University, Linfen, 041000, China
| | - Zengjun Qi
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
30
|
Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
Collapse
|