1
|
Liu X, Xu Z, Feng B, Zhou Q, Guo S, Liao S, Ou Y, Fan X, Wang T. Dissection of a novel major stable QTL on chromosome 7D for grain hardness and its breeding value estimation in bread wheat. FRONTIERS IN PLANT SCIENCE 2024; 15:1356687. [PMID: 38362452 PMCID: PMC10867189 DOI: 10.3389/fpls.2024.1356687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 01/18/2024] [Indexed: 02/17/2024]
Abstract
Grain hardness (Gh) is important for wheat processing and end-product quality. Puroindolines polymorphism explains over 60% of Gh variation and the novel genetic factors remain to be exploited. In this study, a total of 153 quantitative trait loci (QTLs), clustered into 12 genomic intervals (C1-C12), for 13 quality-related traits were identified using a recombinant inbred line population derived from the cross of Zhongkemai138 (ZKM138) and Chuanmai44 (CM44). Among them, C7 (harboring eight QTLs for different quality-related traits) and C8 (mainly harboring QGh.cib-5D.1 for Gh) were attributed to the famous genes, Rht-D1 and Pina, respectively, indicating that the correlation of involved traits was supported by the pleotropic or linked genes. Notably, a novel major stable QTL for Gh was detected in the C12, QGh.cib-7D, with ZKM138-derived allele increasing grain hardness, which was simultaneously mapped by the BSE-Seq method. The geographic pattern and transmissibility of this locus revealed that the increasing-Gh allele is highly frequently present in 85.79% of 373 worldwide wheat varieties and presented 99.31% transmissibility in 144 ZKM138-derivatives, indicating the non-negative effect on yield performance and that its indirect passive selection has happened during the actual breeding process. Thus, the contribution of this new Gh-related locus was highlighted in consideration of improving the efficiency and accuracy of the soft/hard material selection in the molecular marker-assisted process. Further, TraesCS7D02G099400, TraesCS7D02G098000, and TraesCS7D02G099500 were initially deduced to be the most potential candidate genes of QGh.cib-7D. Collectively, this study provided valuable information of elucidating the genetic architecture of Gh for wheat quality improvement.
Collapse
Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Insitute of Plant Protection, Sichuan Academy of Agricultural Science, Chengdu, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuhao Ou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
2
|
Liu P, Liu Z, Ma X, Wan H, Zheng J, Luo J, Deng Q, Mao Q, Li X, Pu Z. Characterization and Differentiation of Grain Proteomes from Wild-Type Puroindoline and Variants in Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:1979. [PMID: 37653896 PMCID: PMC10224366 DOI: 10.3390/plants12101979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 05/06/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Premium wheat with a high end-use quality is generally lacking in China, especially high-quality hard and soft wheat. Pina-D1 and Pinb-D1 (puroindoline genes) influence wheat grain hardness (i.e., important wheat quality-related parameter) and are among the main targets in wheat breeding programs. However, the mechanism by which puroindoline genes control grain hardness remains unclear. In this study, three hard wheat puroindoline variants (MY26, GX3, and ZM1) were compared with a soft wheat variety (CM605) containing the wild-type puroindoline genotype. Specifically, proteomic methods were used to screen for differentially abundant proteins (DAPs). In total, 6253 proteins were identified and quantified via a high-throughput tandem mass tag quantitative proteomic analysis. Of the 208 DAPs, 115, 116, and 99 proteins were differentially expressed between MY26, GX3, and ZM1 (hard wheat varieties) and CM605, respectively. The cluster analysis of protein relative abundances divided the proteins into six clusters. Of these proteins, 67 and 41 proteins were, respectively, more and less abundant in CM605 than in MY26, GX3, and ZM1. Enrichment analyses detected six GO terms, five KEGG pathways, and five IPR terms that were shared by all three comparisons. Furthermore, 12 proteins associated with these terms or pathways were found to be differentially expressed in each comparison. These proteins, which included cysteine proteinase inhibitors, invertases, low-molecular-weight glutenin subunits, and alpha amylase inhibitors, may be involved in the regulation of grain hardness. The candidate genes identified in this study may be relevant for future analyses of the regulatory mechanism underlying grain hardness.
Collapse
Affiliation(s)
- Peixun Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Zehou Liu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Xiaofei Ma
- Wheat Research Institute, Shanxi Agricultural University, Linfen 041000, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Jianmin Zheng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Jiangtao Luo
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Qingyan Deng
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Qiang Mao
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Xiaoye Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| | - Zongjun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Environmentally Friendly Crop Germplasm Innovation and Genetic Improvement Key Laboratory of Sichuan Province, Key Laboratory of Wheat Biology and Genetic Improvement on Southwestern China, Ministry of Agriculture and Rural Areas, Chengdu 610066, China; (P.L.)
| |
Collapse
|
3
|
Melnikova DN, Finkina EI, Bogdanov IV, Tagaev AA, Ovchinnikova TV. Features and Possible Applications of Plant Lipid-Binding and Transfer Proteins. MEMBRANES 2022; 13:2. [PMID: 36676809 PMCID: PMC9866449 DOI: 10.3390/membranes13010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
In plants, lipid trafficking within and inside the cell is carried out by lipid-binding and transfer proteins. Ligands for these proteins are building and signaling lipid molecules, secondary metabolites with different biological activities due to which they perform diverse functions in plants. Many different classes of such lipid-binding and transfer proteins have been found, but the most common and represented in plants are lipid transfer proteins (LTPs), pathogenesis-related class 10 (PR-10) proteins, acyl-CoA-binding proteins (ACBPs), and puroindolines (PINs). A low degree of amino acid sequence homology but similar spatial structures containing an internal hydrophobic cavity are common features of these classes of proteins. In this review, we summarize the latest known data on the features of these protein classes with particular focus on their ability to bind and transfer lipid ligands. We analyzed the structural features of these proteins, the diversity of their possible ligands, the key amino acids participating in ligand binding, the currently known mechanisms of ligand binding and transferring, as well as prospects for possible application.
Collapse
Affiliation(s)
- Daria N. Melnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| | - Ekaterina I. Finkina
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Ivan V. Bogdanov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Andrey A. Tagaev
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Tatiana V. Ovchinnikova
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, the Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology (State University), 141701 Dolgoprudny, Russia
| |
Collapse
|
4
|
Tu M, Li Y. Toward the Genetic Basis and Multiple QTLs of Kernel Hardness in Wheat. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1631. [PMID: 33255282 PMCID: PMC7760206 DOI: 10.3390/plants9121631] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/03/2022]
Abstract
Kernel hardness is one of the most important single traits of wheat seed. It classifies wheat cultivars, determines milling quality and affects many end-use qualities. Starch granule surfaces, polar lipids, storage protein matrices and Puroindolines potentially form a four-way interaction that controls wheat kernel hardness. As a genetic factor, Puroindoline polymorphism explains over 60% of the variation in kernel hardness. However, genetic factors other than Puroindolines remain to be exploited. Over the past two decades, efforts using population genetics have been increasing, and numerous kernel hardness-associated quantitative trait loci (QTLs) have been identified on almost every chromosome in wheat. Here, we summarize the state of the art for mapping kernel hardness. We emphasize that these steps in progress have benefitted from (1) the standardized methods for measuring kernel hardness, (2) the use of the appropriate germplasm and mapping population, and (3) the improvements in genotyping methods. Recently, abundant genomic resources have become available in wheat and related Triticeae species, including the high-quality reference genomes and advanced genotyping technologies. Finally, we provide perspectives on future research directions that will enhance our understanding of kernel hardness through the identification of multiple QTLs and will address challenges involved in fine-tuning kernel hardness and, consequently, food properties.
Collapse
Affiliation(s)
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA;
| |
Collapse
|
5
|
Li X, Li Y, Yu X, Sun F, Yang G, He G. Genomics-Enabled Analysis of Puroindoline b2 Genes Identifies New Alleles in Wheat and Related Triticeae Species. Int J Mol Sci 2020; 21:E1304. [PMID: 32075191 PMCID: PMC7072932 DOI: 10.3390/ijms21041304] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 02/07/2020] [Accepted: 02/11/2020] [Indexed: 01/12/2023] Open
Abstract
Kernel hardness is a key trait of wheat seeds, largely controlled by two tightly linked genes Puroindoline a and b (Pina and Pinb). Genes homologous to Pinb, namely Pinb2, have been studied. Whether these genes contribute to kernel hardness and other important seed traits remains inconclusive. Using the high-quality bread wheat reference genome, we show that PINB2 are encoded by three homoeologous loci Pinb2 not syntenic to the Hardness locus, with Pinb2-7A locus containing three tandem copies. PINB2 proteins have several features conserved for the Pin/Pinb2 phylogenetic cluster but lack a structural basis of significant impact on kernel hardness. Pinb2 are seed-specifically expressed with varied expression levels between the homoeologous copies and among wheat varieties. Using the high-quality genome information, we developed new Pinb2 allele specific markers and demonstrated their usefulness by 1) identifying new Pinb2 alleles in Triticeae species; and 2) performing an association analysis of Pinb2 with kernel hardness. The association result suggests that Pinb2 genes may have no substantial contribution to kernel hardness. Our results provide new insights into Pinb2 evolution and expression and the new allele-specific markers are useful to further explore Pinb2's contribution to seed traits in wheat.
Collapse
Affiliation(s)
- Xiaoyan Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Yin Li
- Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, 190 Frelinghuysen Road, Piscataway, NJ 08854, USA;
| | - Xiaofen Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Fusheng Sun
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China; (X.L.); (X.Y.); (F.S.)
| |
Collapse
|