1
|
Chen T, Miao Y, Jing F, Gao W, Zhang Y, Zhang L, Zhang P, Guo L, Yang D. Genomic-wide analysis reveals seven in absentia genes regulating grain development in wheat (Triticum aestivum L.). THE PLANT GENOME 2024:e20480. [PMID: 38840306 DOI: 10.1002/tpg2.20480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/28/2024] [Accepted: 05/10/2024] [Indexed: 06/07/2024]
Abstract
Seven in absentia proteins, which contain a conserved SINA domain, are involved in regulating various aspects of wheat (Triticum aestivum L.) growth and development, especially in response to environmental stresses. However, it is unclear whether TaSINA family members are involved in regulating grain development until now. In this study, the expression pattern, genomic polymorphism, and relationship with grain-related traits were analyzed for all TaSINA members. Most of the TaSINA genes identified showed higher expression levels in young wheat spikes or grains than other organs. The genomic polymorphism analysis revealed that at least 62 TaSINA genes had different haplotypes, where the haplotypes of five genes were significantly correlated with grain-related traits. Kompetitive allele-specific PCR markers were developed to confirm the single nucleotide polymorphisms in TaSINA101 and TaSINA109 among the five selected genes in a set of 292 wheat accessions. The TaSINA101-Hap II and TaSINA109-Hap II haplotypes had higher grain weight and width compared to TaSINA101-Hap I and TaSINA109-Hap I in at least three environments, respectively. The qRT-PCR assays revealed that TaSINA101 was highly expressed in the palea shell, seed coat, and embryo in young wheat grains. The TaSINA101 protein was unevenly distributed in the nucleus when transiently expressed in the protoplast of wheat. Three homozygous TaSINA101 transgenic lines in rice (Oryza sativa L.) showed higher grain weight and size compared to the wild type. These findings provide valuable insight into the biological function and elite haplotype of TaSINA family genes in wheat grain development at a genomic-wide level.
Collapse
Affiliation(s)
- Tao Chen
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yongping Miao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fanli Jing
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weidong Gao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yanyan Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Long Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Lijian Guo
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|
2
|
Li Y, Hu J, Qu Y, Qiu D, Lin H, Du J, Hou L, Ma L, Wu Q, Zhou Y, Zhang H, Yang L, Liu H, Liu Z, Zhou Y, Li H. Alleles on locus chromosome 4B from different parents confer tiller number and the yield-associated traits in wheat. BMC PLANT BIOLOGY 2024; 24:454. [PMID: 38789943 PMCID: PMC11127307 DOI: 10.1186/s12870-024-05079-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/28/2024] [Indexed: 05/26/2024]
Abstract
Pleiotropy is frequently detected in agronomic traits of wheat (Triticum aestivum). A locus on chromosome 4B, QTn/Ptn/Sl/Sns/Al/Tgw/Gl/Gw.caas-4B, proved to show pleiotropic effects on tiller, spike, and grain traits using a recombinant inbred line (RIL) population of Qingxinmai × 041133. The allele from Qingxinmai increased tiller numbers, and the allele from line 041133 produced better performances of spike traits and grain traits. Another 52 QTL for the eight traits investigated were detected on 18 chromosomes, except for chromosomes 5D, 6D, and 7B. Several genes in the genomic interval of the locus on chromosome 4B were differentially expressed in crown and inflorescence samples between Qingxinmai and line 041133. The development of the KASP marker specific for the locus on chromosome 4B is useful for molecular marker-assisted selection in wheat breeding.
Collapse
Affiliation(s)
- Yahui Li
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jinghuang Hu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunfeng Qu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Dan Qiu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huailong Lin
- Jiushenghe Seed Industry Co. Ltd, Changji, 831100, China
| | - Jiuyuan Du
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, 730070, China
| | - Lu Hou
- Key Laboratory of Agricultural Integrated Pest Management, Qinghai Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, 810016, China
| | - Lin Ma
- Datong Hui and Tu Autonomous County Agricultural Technology Extension Center, Xining, 810100, China
| | - Qiuhong Wu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yang Zhou
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongjun Zhang
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Li Yang
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongwei Liu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yijun Zhou
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
3
|
Hong Y, Zhang M, Yuan Z, Zhu J, Lv C, Guo B, Wang F, Xu R. Genome-wide association studies reveal stable loci for wheat grain size under different sowing dates. PeerJ 2024; 12:e16984. [PMID: 38426132 PMCID: PMC10903348 DOI: 10.7717/peerj.16984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024] Open
Abstract
Background Wheat (Tritium aestivum L.) production is critical for global food security. In recent years, due to climate change and the prolonged growing period of rice varieties, the delayed sowing of wheat has resulted in a loss of grain yield in the area of the middle and lower reaches of the Yangtze River. It is of great significance to screen for natural germplasm resources of wheat that are resistant to late sowing and to explore genetic loci that stably control grain size and yield. Methods A collection of 327 wheat accessions from diverse sources were subjected to genome-wide association studies using genotyping-by-sequencing. Field trials were conducted under normal, delayed, and seriously delayed sowing conditions for grain length, width, and thousand-grain weight at two sites. Additionally, the additive main effects and multiplicative interaction (AMMI) model was applied to evaluate the stability of thousand-grain weight of 327 accessions across multiple sowing dates. Results Four wheat germplasm resources have been screened, demonstrating higher stability of thousand-grain weight. A total of 43, 35, and 39 significant MTAs were determined across all chromosomes except for 4D under the three sowing dates, respectively. A total of 10.31% of MTAs that stably affect wheat grain size could be repeatedly identified in at least two sowing dates, with PVE ranging from 0.03% to 38.06%. Among these, six were for GL, three for GW, and one for TGW. There were three novel and stable loci (4A_598189950, 4B_307707920, 2D_622241054) located in conserved regions of the genome, which provide excellent genetic resources for pyramid breeding strategies of superior loci. Our findings offer a theoretical basis for cultivar improvement and marker-assisted selection in wheat breeding practices.
Collapse
Affiliation(s)
- Yi Hong
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laborat, Yangzhou University, Yangzhou, China
| | - Mengna Zhang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laborat, Yangzhou University, Yangzhou, China
| | - Zechen Yuan
- Jiangsu Internet Agricultural Development Center, Nanjing, China
| | - Juan Zhu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laborat, Yangzhou University, Yangzhou, China
| | - Chao Lv
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laborat, Yangzhou University, Yangzhou, China
| | - Baojian Guo
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laborat, Yangzhou University, Yangzhou, China
| | - Feifei Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laborat, Yangzhou University, Yangzhou, China
| | - Rugen Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Joint International Research Laborat, Yangzhou University, Yangzhou, China
| |
Collapse
|
4
|
Sharma D, Kumari A, Sharma P, Singh A, Sharma A, Mir ZA, Kumar U, Jan S, Parthiban M, Mir RR, Bhati P, Pradhan AK, Yadav A, Mishra DC, Budhlakoti N, Yadav MC, Gaikwad KB, Singh AK, Singh GP, Kumar S. Meta-QTL analysis in wheat: progress, challenges and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:247. [PMID: 37975911 DOI: 10.1007/s00122-023-04490-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Wheat, an important cereal crop globally, faces major challenges due to increasing global population and changing climates. The production and productivity are challenged by several biotic and abiotic stresses. There is also a pressing demand to enhance grain yield and quality/nutrition to ensure global food and nutritional security. To address these multifaceted concerns, researchers have conducted numerous meta-QTL (MQTL) studies in wheat, resulting in the identification of candidate genes that govern these complex quantitative traits. MQTL analysis has successfully unraveled the complex genetic architecture of polygenic quantitative traits in wheat. Candidate genes associated with stress adaptation have been pinpointed for abiotic and biotic traits, facilitating targeted breeding efforts to enhance stress tolerance. Furthermore, high-confidence candidate genes (CGs) and flanking markers to MQTLs will help in marker-assisted breeding programs aimed at enhancing stress tolerance, yield, quality and nutrition. Functional analysis of these CGs can enhance our understanding of intricate trait-related genetics. The discovery of orthologous MQTLs shared between wheat and other crops sheds light on common evolutionary pathways governing these traits. Breeders can leverage the most promising MQTLs and CGs associated with multiple traits to develop superior next-generation wheat cultivars with improved trait performance. This review provides a comprehensive overview of MQTL analysis in wheat, highlighting progress, challenges, validation methods and future opportunities in wheat genetics and breeding, contributing to global food security and sustainable agriculture.
Collapse
Affiliation(s)
- Divya Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anita Kumari
- Department of Botany, University of Delhi, Delhi, India
| | - Priya Sharma
- Department of Botany, University of Delhi, Delhi, India
| | - Anupma Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Anshu Sharma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Zahoor Ahmad Mir
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Sofora Jan
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - M Parthiban
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Reyazul Rouf Mir
- Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, Kashmir, India
| | - Pradeep Bhati
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | - Anjan Kumar Pradhan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Aakash Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Neeraj Budhlakoti
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mahesh C Yadav
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | - Kiran B Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, India.
| |
Collapse
|
5
|
Valladares García AP, Desiderio F, Simeone R, Ravaglia S, Ciorba R, Fricano A, Guerra D, Blanco A, Cattivelli L, Mazzucotelli E. QTL mapping for kernel-related traits in a durum wheat x T. dicoccum segregating population. FRONTIERS IN PLANT SCIENCE 2023; 14:1253385. [PMID: 37849841 PMCID: PMC10577384 DOI: 10.3389/fpls.2023.1253385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 10/19/2023]
Abstract
Durum wheat breeding relies on grain yield improvement to meet its upcoming demand while coping with climate change. Kernel size and shape are the determinants of thousand kernel weight (TKW), which is a key component of grain yield, and the understanding of the genetic control behind these traits supports the progress in yield potential. The present study aimed to dissect the genetic network responsible for kernel size components (length, width, perimeter, and area) and kernel shape traits (width-to-length ratio and formcoefficient) as well as their relationships with kernel weight, plant height, and heading date in durum wheat. Quantitative Trait Locus (QTL) mapping was performed on a segregating population of 110 recombinant inbred lines, derived from a cross between the domesticated emmer wheat accession MG5323 and the durum wheat cv. Latino, evaluated in four different environments. A total of 24 QTLs stable across environments were found and further grouped in nine clusters on chromosomes 2A, 2B, 3A, 3B, 4B, 6B, and 7A. Among them, a QTL cluster on chromosome 4B was associated with kernel size traits and TKW, where the parental MG5323 contributed the favorable alleles, highlighting its potential to improve durum wheat germplasm. The physical positions of the clusters, defined by the projection on the T. durum reference genome, overlapped with already known genes (i.e., BIG GRAIN PROTEIN 1 on chromosome 4B). These results might provide genome-based guidance for the efficient exploitation of emmer wheat diversity in wheat breeding, possibly through yield-related molecular markers.
Collapse
Affiliation(s)
- Ana Paola Valladares García
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana (COMAV), Universitat Politècnica de València, Valencia, Spain
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Francesca Desiderio
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Rosanna Simeone
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | | | - Roberto Ciorba
- Council for Agricultural Research and Economics (CREA) - Research Centre for Olive, Fruit and Citrus Crops, Rome, Italy
| | - Agostino Fricano
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Antonio Blanco
- Department of Soil, Plant and Food Sciences (DiSSPA), Genetics and Plant Breeding Section, University of Bari Aldo Moro, Bari, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics (CREA) - Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| |
Collapse
|
6
|
Navea IP, Maung PP, Yang S, Han JH, Jing W, Shin NH, Zhang W, Chin JH. A meta-QTL analysis highlights genomic hotspots associated with phosphorus use efficiency in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1226297. [PMID: 37662146 PMCID: PMC10471825 DOI: 10.3389/fpls.2023.1226297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023]
Abstract
Phosphorus use efficiency (PUE) is a complex trait, governed by many minor quantitative trait loci (QTLs) with small effects. Advances in molecular marker technology have led to the identification of QTLs underlying PUE. However, their practical use in breeding programs remains challenging due to the unstable effects in different genetic backgrounds and environments, interaction with soil status, and linkage drag. Here, we compiled PUE QTL information from 16 independent studies. A total of 192 QTLs were subjected to meta-QTL (MQTL) analysis and were projected into a high-density SNP consensus map. A total of 60 MQTLs, with significantly reduced number of initial QTLs and confidence intervals (CI), were identified across the rice genome. Candidate gene (CG) mining was carried out for the 38 MQTLs supported by multiple QTLs from at least two independent studies. Genes related to amino and organic acid transport and auxin response were found to be abundant in the MQTLs linked to PUE. CGs were cross validated using a root transcriptome database (RiceXPro) and haplotype analysis. This led to the identification of the eight CGs (OsARF8, OsSPX-MFS3, OsRING141, OsMIOX, HsfC2b, OsFER2, OsWRKY64, and OsYUCCA11) modulating PUE. Potential donors for superior PUE CG haplotypes were identified through haplotype analysis. The distribution of superior haplotypes varied among subspecies being mostly found in indica but were largely scarce in japonica. Our study offers an insight on the complex genetic networks that modulate PUE in rice. The MQTLs, CGs, and superior CG haplotypes identified in our study are useful in the combination of beneficial alleles for PUE in rice.
Collapse
Affiliation(s)
- Ian Paul Navea
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| | - Phyu Phyu Maung
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| | - Shiyi Yang
- College of Life Sciences, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jae-Hyuk Han
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- The International Rice Research Institute-Korea Office, National Institute of Crop Science, Rural Development Administration, Iseo-myeon, Republic of Korea
| | - Wen Jing
- College of Life Sciences, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Na-Hyun Shin
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| | - Wenhua Zhang
- College of Life Sciences, National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Joong Hyoun Chin
- Food Crops Molecular Breeding Laboratory, Department of Integrative Biological Sciences and Industry, Sejong University, Seoul, Republic of Korea
- Convergence Research Center for Natural Products, Sejong University, Seoul, Republic of Korea
| |
Collapse
|
7
|
Mroz T, Dieseth JA, Lillemo M. Grain yield and adaptation of spring wheat to Norwegian growing conditions is driven by allele frequency changes at key adaptive loci discovered by genome-wide association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:191. [PMID: 37589760 PMCID: PMC10435424 DOI: 10.1007/s00122-023-04424-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/24/2023] [Indexed: 08/18/2023]
Abstract
KEY MESSAGE Adaptation to the Norwegian environment is associated with polymorphisms in the Vrn-A1 locus. Historical selection for grain yield in Nordic wheat is associated with TaGS5-3A and TaCol-5 loci. Grain yields in Norwegian spring wheat increased by 18 kg ha-1 per year between 1972 and 2019 due to introduction of new varieties. These gains were associated with increments in the number of grains per spike and extended length of the vegetative period. However, little is known about the genetic background of this progress. To fill this gap, we conducted genome-wide association study on a panel consisting of both adapted (historical and current varieties and lines in the Nordics) and important not adapted accessions used as parents in the Norwegian wheat breeding program. The study concerned grain yield, plant height, and heading and maturity dates, and detected 12 associated loci, later validated using independent sets of recent breeding lines. Adaptation to the Norwegian cropping conditions was found to be associated with the Vrn-A1 locus, and a previously undescribed locus on chromosome 1B associated with heading date. Two loci associated with grain yield, corresponding to the TaGS5-3A and TaCol-5 loci, indicated historical selection pressure for high grain yield. A locus on chromosome 2A explained the tallness of the oldest accessions. We investigated the origins of the beneficial alleles associated with the wheat breeding progress in the Norwegian material, tracing them back to crosses with Swedish, German, or CIMMYT lines. This study contributes to the understanding of wheat adaptation to the Norwegian growing conditions, sheds light on the genetic basis of historical wheat improvement and aids future breeding efforts by discovering loci associated with important agronomic traits in wheat.
Collapse
Affiliation(s)
- Tomasz Mroz
- Department of Plant Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Jon Arne Dieseth
- Graminor, AS, Bjørke Gård, Hommelstadvegen 60, 2322, Ridabu, Norway
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, 1432, Ås, Norway.
| |
Collapse
|
8
|
Bilgrami S, Darzi Ramandi H, Farokhzadeh S, Rousseau-Gueutin M, Sobhani Najafabadi A, Ghaderian M, Huang P, Liu L. Meta-analysis of seed weight QTLome using a consensus and highly dense genetic map in Brassica napus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:161. [PMID: 37354229 DOI: 10.1007/s00122-023-04401-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 06/02/2023] [Indexed: 06/26/2023]
Abstract
KEY MESSAGE We report here the discovery of high-confidence MQTL regions and of putative candidate genes associated with seed weight in B. napus using a highly dense consensus genetic map and by comparing various large-scale multiomics datasets. Seed weight (SW) is a direct determinant of seed yield in Brassica napus and is controlled by many loci. To unravel the main genomic regions associated with this complex trait, we used 13 available genetic maps to construct a consensus and highly dense map, comprising 40,401 polymorphic markers and 9191 genetic bins, harboring a cumulative length of 3047.8 cM. Then, we performed a meta-analysis using 639 projected SW quantitative trait loci (QTLs) obtained from studies conducted since 1999, enabling the identification of 57 meta-QTLS (MQTLs). The confidence intervals of our MQTLs were 9.8 and 4.3 times lower than the average CIs of the original QTLs for the A and C subgenomes, respectively, resulting in the detection of some key genes and several putative novel candidate genes associated with SW. By comparing the genes identified in MQTL intervals with multiomics datasets and coexpression analyses of common genes, we defined a more reliable and shorter list of putative candidate genes potentially involved in the regulation of seed maturation and SW. As an example, we provide a list of promising genes with high expression levels in seeds and embryos (e.g., BnaA03g04230D, BnaC03g08840D, BnaA10g29580D and BnaA03g27410D) that can be more finely studied through functional genetics experiments or that may be useful for MQTL-assisted breeding for SW. The high-density genetic consensus map and the single nucleotide polymorphism (SNP) physical map generated from the latest B. napus cv. Darmor-bzh v10 assembly will be a valuable resource for further mapping and map-based cloning of other important traits.
Collapse
Affiliation(s)
- Sayedehsaba Bilgrami
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Hadi Darzi Ramandi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran
| | - Sara Farokhzadeh
- Department of Plant Production, College of Agriculture and Natural Resources of Darab, Shiraz University, Darab, Iran
| | | | - Ahmad Sobhani Najafabadi
- Department of Biotechnology, Agricultural Biotechnology Research Institute of Iran - Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Mostafa Ghaderian
- Division of Biostatistics and Bioinformatics, Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, 45220, USA
| | - Pu Huang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
| |
Collapse
|
9
|
Wang K, Shi L, Zheng B, He Y. Responses of wheat kernel weight to diverse allelic combinations under projected climate change conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1138966. [PMID: 36998681 PMCID: PMC10043320 DOI: 10.3389/fpls.2023.1138966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION In wheat, kernel weight (KW) is a key determinant of grain yield (GY). However, it is often overlooked when improving wheat productivity under climate warming. Moreover, little is known about the complex effects of genetic and climatic factors on KW. Here, we explored the responses of wheat KW to diverse allelic combinations under projected climate warming conditions. METHODS To focus on KW, we selected a subset of 81 out of 209 wheat varieties with similar GY, biomass, and kernel number (KN) and focused on their thousand-kernel weight (TKW). We genotyped them at eight kompetitive allele-specific polymerase chain reaction markers closely associated with TKW. Subsequently, we calibrated and evaluated the process-based model known as Agricultural Production Systems Simulator (APSIM-Wheat) based on a unique dataset including phenotyping, genotyping, climate, soil physicochemistry, and on-farm management information. We then used the calibrated APSIM-Wheat model to estimate TKW under eight allelic combinations (81 wheat varieties), seven sowing dates, and the shared socioeconomic pathways (SSPs) designated SSP2-4.5 and SSP5-8.5, driven by climate projections from five General Circulation Models (GCMs) BCC-CSM2-MR, CanESM5, EC-Earth3-Veg, MIROC-ES2L, and UKESM1-0-LL. RESULTS The APSIM-Wheat model reliably simulated wheat TKW with a root mean square error (RMSE) of < 3.076 g TK-1 and R2 of > 0.575 (P < 0.001). The analysis of variance based on the simulation output showed that allelic combination, climate scenario, and sowing date extremely significantly affected TKW (P < 0.001). The impact of the interaction allelic combination × climate scenario on TKW was also significant (P < 0.05). Meanwhile, the variety parameters and their relative importance in the APSIM-Wheat model accorded with the expression of the allelic combinations. Under the projected climate scenarios, the favorable allelic combinations (TaCKX-D1b + Hap-7A-1 + Hap-T + Hap-6A-G + Hap-6B-1 + H1g + A1b for SSP2-4.5 and SSP5-8.5) mitigated the negative effects of climate change on TKW. DISCUSSION The present study demonstrated that optimizing favorable allelic combinations can help achieve high wheat TKW. The findings of this study clarify the responses of wheat KW to diverse allelic combinations under projected climate change conditions. Additionally, the present study provides theoretical and practical reference for marker-assisted selection of high TKW in wheat breeding.
Collapse
Affiliation(s)
- Keyi Wang
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liping Shi
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bangyou Zheng
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Biosciences Precinct, St. Lucia, QLD, Australia
| | - Yong He
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
10
|
Guo K, Chen T, Zhang P, Liu Y, Che Z, Shahinnia F, Yang D. Meta-QTL analysis and in-silico transcriptome assessment for controlling chlorophyll traits in common wheat. THE PLANT GENOME 2023; 16:e20294. [PMID: 36636827 DOI: 10.1002/tpg2.20294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/02/2022] [Indexed: 05/10/2023]
Abstract
Chlorophyll is an important plant molecule for absorbing light and transferring electrons to produce energy for photosynthesis, which has a significant impact on crop yield. To identify quantitative trait loci (QTL) controlling chlorophyll traits in wheat (Triticum aestivum L.), a comprehensive meta-analysis of 411 original QTLs for six chlorophyll traits was performed, including the evolution of soil plant analysis development (SPAD), chlorophyll content index (CCI), chlorophyll a content (Chla), chlorophyll b content (Chlb), chlorophyll content (Chl), and ratio of chlorophyll a to b (Chla/b), derived from 41 independent experiments conducted over the past two decades. Fifty-six consensus meta-QTLs (MQTLs) were detected, unevenly distributed on chromosomes 1A, 1B, 2A, 2B, 2D, 3B, 3D, 4B, 4D, 5A, 5D, 6A, 6D, 7B, and 7D. The confidence interval (CI) of the identified MQTLs was 0.18 to 15.07 cM, with an average of 5.74 cM, and 3.17-times narrower than that of the original QTLs. A total of 30 MQTLs were aligned with marker-trait associations (MTAs) reported in genome-wide association studies (GWAS) for chlorophyll traits in wheat. Based on MQTL-flanking marker information and homology analyses combined with RNA-seq data, 136 putative candidate genes were identified in MQTL regions, involved in porphyrin metabolism, photosynthesis, terpene biosynthesis, glyoxylate and dicarboxylate metabolism, and secondary metabolites. The results of this study contribute to the understanding of the genetic basis for controlling chlorophyll traits and can be used in breeding wheat with high photosynthetic efficiency.
Collapse
Affiliation(s)
- Kaiqi Guo
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
| | - Tao Chen
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
| | - Yuan Liu
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Lanzhou, 730000, China
| | - Fahimeh Shahinnia
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, Freising, 85354, Germany
| | - Delong Yang
- State Key Lab of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural Univ., Lanzhou, 730070, China
| |
Collapse
|
11
|
Kong B, Ma J, Zhang P, Chen T, Liu Y, Che Z, Shahinnia F, Yang D. Deciphering key genomic regions controlling flag leaf size in wheat via integration of meta-QTL and in silico transcriptome assessment. BMC Genomics 2023; 24:33. [PMID: 36658498 PMCID: PMC9854125 DOI: 10.1186/s12864-023-09119-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Grain yield is a complex and polygenic trait influenced by the photosynthetic source-sink relationship in wheat. The top three leaves, especially the flag leaf, are considered the major sources of photo-assimilates accumulated in the grain. Determination of significant genomic regions and candidate genes affecting flag leaf size can be used in breeding for grain yield improvement. RESULTS With the final purpose of understanding key genomic regions for flag leaf size, a meta-analysis of 521 initial quantitative trait loci (QTLs) from 31 independent QTL mapping studies over the past decades was performed, where 333 loci eventually were refined into 64 meta-QTLs (MQTLs). The average confidence interval (CI) of these MQTLs was 5.28 times less than that of the initial QTLs. Thirty-three MQTLs overlapped the marker trait associations (MTAs) previously reported in genome-wide association studies (GWAS) for flag leaf traits in wheat. A total of 2262 candidate genes for flag leaf size, which were involved in the peroxisome, basal transcription factor, and tyrosine metabolism pathways were identified in MQTL regions by the in silico transcriptome assessment. Of these, the expression analysis of the available genes revealed that 134 genes with > 2 transcripts per million (TPM) were highly and specifically expressed in the leaf. These candidate genes could be critical to affect flag leaf size in wheat. CONCLUSIONS The findings will make further insight into the genetic determinants of flag leaf size and provide some reliable MQTLs and putative candidate genes for the genetic improvement of flag leaf size in wheat.
Collapse
Affiliation(s)
- Binxue Kong
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yuan Liu
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Zhuo Che
- Plant Seed Master Station of Gansu Province, Lanzhou, 730000, China
| | - Fahimeh Shahinnia
- Bavarian State Research Centre for Agriculture, Institute for Crop Science and Plant Breeding, 85354, Freising, Germany
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| |
Collapse
|
12
|
Aloryi KD, Okpala NE, Amo A, Bello SF, Akaba S, Tian X. A meta-quantitative trait loci analysis identified consensus genomic regions and candidate genes associated with grain yield in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1035851. [PMID: 36466247 PMCID: PMC9709451 DOI: 10.3389/fpls.2022.1035851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/19/2022] [Indexed: 06/17/2023]
Abstract
Improving grain yield potential in rice is an important step toward addressing global food security challenges. The meta-QTL analysis offers stable and robust QTLs irrespective of the genetic background of mapping populations and phenotype environment and effectively narrows confidence intervals (CI) for candidate gene (CG) mining and marker-assisted selection improvement. To achieve these aims, a comprehensive bibliographic search for grain yield traits (spikelet fertility, number of grains per panicle, panicles number per plant, and 1000-grain weight) QTLs was conducted, and 462 QTLs were retrieved from 47 independent QTL research published between 2002 and 2022. QTL projection was performed using a reference map with a cumulative length of 2,945.67 cM, and MQTL analysis was conducted on 313 QTLs. Consequently, a total of 62 MQTLs were identified with reduced mean CI (up to 3.40 fold) compared to the mean CI of original QTLs. However, 10 of these MQTLs harbored at least six of the initial QTLs from diverse genetic backgrounds and environments and were considered the most stable and robust MQTLs. Also, MQTLs were compared with GWAS studies and resulted in the identification of 16 common significant loci modulating the evaluated traits. Gene annotation, gene ontology (GO) enrichment, and RNA-seq analyses of chromosome regions of the stable MQTLs detected 52 potential CGs including those that have been cloned in previous studies. These genes encode proteins known to be involved in regulating grain yield including cytochrome P450, zinc fingers, MADs-box, AP2/ERF domain, F-box, ubiquitin ligase domain protein, homeobox domain, DEAD-box ATP domain, and U-box domain. This study provides the framework for molecular dissection of grain yield in rice. Moreover, the MQTLs and CGs identified could be useful for fine mapping, gene cloning, and marker-assisted selection to improve rice productivity.
Collapse
Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Aduragbemi Amo
- Institute of Plant Breeding, Genetics and Genomics University of Georgia, Athens, GA, United States
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| |
Collapse
|
13
|
Tillett BJ, Hale CO, Martin JM, Giroux MJ. Genes Impacting Grain Weight and Number in Wheat ( Triticum aestivum L. ssp. aestivum). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11131772. [PMID: 35807724 PMCID: PMC9269389 DOI: 10.3390/plants11131772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/17/2022] [Accepted: 06/27/2022] [Indexed: 05/05/2023]
Abstract
The primary goal of common wheat (T. aestivum) breeding is increasing yield without negatively impacting the agronomic traits or product quality. Genetic approaches to improve the yield increasingly target genes that impact the grain weight and number. An energetic trade-off exists between the grain weight and grain number, the result of which is that most genes that increase the grain weight also decrease the grain number. QTL associated with grain weight and number have been identified throughout the hexaploid wheat genome, leading to the discovery of numerous genes that impact these traits. Genes that have been shown to impact these traits will be discussed in this review, including TaGNI, TaGW2, TaCKX6, TaGS5, TaDA1, WAPO1, and TaRht1. As more genes impacting the grain weight and number are characterized, the opportunity is increasingly available to improve common wheat agronomic yield by stacking the beneficial alleles. This review provides a synopsis of the genes that impact grain weight and number, and the most beneficial alleles of those genes with respect to increasing the yield in dryland and irrigated conditions. It also provides insight into some of the genetic mechanisms underpinning the trade-off between grain weight and number and their relationship to the source-to-sink pathway. These mechanisms include the plant size, the water soluble carbohydrate levels in plant tissue, the size and number of pericarp cells, the cytokinin and expansin levels in developing reproductive tissue, floral architecture and floral fertility.
Collapse
|
14
|
Wang P, Tian T, Ma J, Liu Y, Zhang P, Chen T, Shahinnia F, Yang D. Genome-Wide Association Study of Kernel Traits Using a 35K SNP Array in Bread Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:905660. [PMID: 35734257 PMCID: PMC9207461 DOI: 10.3389/fpls.2022.905660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Kernel size and weight are crucial components of grain yield in wheat. Deciphering their genetic basis is essential for improving yield potential in wheat breeding. In this study, five kernel traits, including kernel length (KL), kernel width (KW), kernel diameter ratio (KDR), kernel perimeter (KP), and thousand-kernel weight (TKW), were evaluated in a panel consisting of 198 wheat accessions under six environments. Wheat accessions were genotyped using the 35K SNP iSelect chip array, resulting in a set of 13,228 polymorphic SNP markers that were used for genome-wide association study (GWAS). A total of 146 significant marker-trait associations (MTAs) were identified for five kernel traits on 21 chromosomes [-log10(P) ≥ 3], which explained 5.91-15.02% of the phenotypic variation. Of these, 12 stable MTAs were identified in multiple environments, and six superior alleles showed positive effects on KL, KP, and KDR. Four potential candidate genes underlying the associated SNP markers were predicted for encoding ML protein, F-box protein, ethylene-responsive transcription factor, and 1,4-α-glucan branching enzyme. These genes were strongly expressed in grain development at different growth stages. The results will provide new insights into the genetic basis of kernel traits in wheat. The associated SNP markers and predicted candidate genes will facilitate marker-assisted selection in wheat breeding.
Collapse
Affiliation(s)
- Peng Wang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Tian Tian
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jingfu Ma
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yuan Liu
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fahimeh Shahinnia
- Bavarian State Research Center for Agriculture, Institute for Crop Science and Plant Breeding, Freising, Germany
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| |
Collapse
|