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Yang J, Liu Z, Liu Y, Fan X, Gao L, Li Y, Hu Y, Hu K, Huang Y. Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize ( Zea mays L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:1533. [PMID: 38891341 PMCID: PMC11175157 DOI: 10.3390/plants13111533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/15/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
Deep sowing is an efficient strategy for maize to ensure the seedling emergence rate under adverse conditions such as drought or low temperatures. However, the genetic basis of deep-sowing tolerance-related traits in maize remains largely unknown. In this study, we performed a genome-wide association study on traits related to deep-sowing tolerance, including mesocotyl length (ML), coleoptile length (CL), plumule length (PL), shoot length (SL), and primary root length (PRL), using 255 maize inbred lines grown in three different environments. We identified 23, 6, 4, and 4 quantitative trait loci (QTLs) associated with ML, CL, PL, and SL, respectively. By analyzing candidate genes within these QTLs, we found a γ-tubulin-containing complex protein, ZmGCP2, which was significantly associated with ML, PL, and SL. Loss of function of ZmGCP2 resulted in decreased PL, possibly by affecting the cell elongation, thus affecting SL. Additionally, we identified superior haplotypes and allelic variations of ZmGCP2 with a longer PL and SL, which may be useful for breeding varieties with deep-sowing tolerance to improve maize cultivation.
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Affiliation(s)
- Jin Yang
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Zhou Liu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Yanbo Liu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Xiujun Fan
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Lei Gao
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Yangping Li
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Yufeng Hu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
| | - Kun Hu
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
- Sinograin Chengdu Storage Research Institute Co., Ltd., Chengdu 610091, China
| | - Yubi Huang
- State Key Laboratory of Crop Gene Resource Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China; (J.Y.); (Z.L.); (Y.L.); (X.F.); (L.G.); (Y.L.); (Y.H.)
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Liang Z, Xi N, Liu T, Li M, Sang M, Zou C, Chen Z, Yuan G, Pan G, Ma L, Shen Y. A combination of QTL mapping and genome-wide association study revealed the key gene for husk number in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:112. [PMID: 38662228 DOI: 10.1007/s00122-024-04617-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 04/07/2024] [Indexed: 04/26/2024]
Abstract
KEY MESSAGE Two key genes Zm00001d021232 and Zm00001d048138 were identified by QTL mapping and GWAS. Additionally, they were verified to be significantly associated with maize husk number (HN) using gene-based association study. As a by-product of maize production, maize husk is an important industrial raw material. Husk layer number (HN) is an important trait that affects the yield of maize husk. However, the genetic mechanism underlying HN remains unclear. Herein, a total of 13 quantitative trait loci (QTL) controlling HN were identified in an IBM Syn 10 DH population across different locations. Among these, three QTL were individually repeatedly detected in at least two environments. Meanwhile, 26 unique single nucleotide polymorphisms (SNPs) were detected to be significantly (p < 2.15 × 10-6) associated with HN in an association pool. Of these SNPs, three were simultaneously detected across multiple environments or environments and best linear unbiased prediction (BLUP). We focused on these environment-stable and population-common genetic loci for excavating the candidate genes responsible for maize HN. Finally, 173 initial candidate genes were identified, of which 22 were involved in both multicellular organism development and single-multicellular organism process and thus confirmed as the candidate genes for HN. Gene-based association analyses revealed that the variants in four genes were significantly (p < 0.01/N) correlated with HN, of which Zm00001d021232 and Zm00001d048138 were highly expressed in husks and early developing ears among different maize tissues. Our study contributes to the understanding of genetic and molecular mechanisms of maize husk yield and industrial development in the future.
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Affiliation(s)
- Zhenjuan Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Na Xi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minglin Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Mengxiang Sang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhong Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangsheng Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Kumawat G, Jakhar ML, Singh V, Singh J, Gothwal DK, Yadava DK. High throughput phenotyping of functional traits and key indices for selection of salt tolerant Mustard [Brassica juncea (L.) Czern & Coss] genotypes. PHYSIOLOGIA PLANTARUM 2024; 176:e14178. [PMID: 38342492 DOI: 10.1111/ppl.14178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/15/2023] [Accepted: 12/19/2023] [Indexed: 02/13/2024]
Abstract
The current scanty knowledge about the salt tolerance mechanism underlying the ability of plants to tolerate salt stress hinders the potential production of numerous crops, including Indian mustard. To explore the traits and mechanism for salt tolerance, high throughput phenotyping of 250 stabilized F7:8 recombinant inbred lines (RILs) mapping population of Indian mustard were conducted under control and salinity (ECiw 12 dS m-1 ) for 54 morpho-physio-seed-quality traits. Most of the traits were reduced with variable percentages under salt stress. The stress tolerance index (STI) of YPP showed a significant negative association with Na+ concentration of root (RNa), indicating that RILs with low Na+ concentration have high seed yield and a positive significant association with STI of yield-related traits, photosynthesis rate (Pn), intrinsic water use efficiency (inWUE), fresh weight of upper leaf (USFW), fresh weight of branches (BrFW), fresh weight of basal leaf (BLFW), and fresh weight of middle leaf (MLFW) revealed that by improving these traits seed yield per plant (YPP) was improved. Based on principal component analysis (PCA) of 54 STI and new index composite selection index (CSI), RILs viz., R114, R150, R164, R170, and R206 were identified as stable performers which can be exploited for quantitative trait loci (QTLs)/gene discovery and serve as potential donors to combat salt stress. Our research will serve to determine the relative importance of different functional traits of salt tolerance mechanisms that can be used to screen colossal germplasm.
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Affiliation(s)
- Gayatri Kumawat
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Rajasthan, India
- Livestock Feed Resource Management and Technology Centre, Rajasthan University of Veterinary and Animal Sciences, Bikaner, India
| | - Mohan Lal Jakhar
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Rajasthan, India
| | - Vijayata Singh
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
| | - Jogendra Singh
- Division of Crop Improvement, ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India
| | - Dinesh Kumar Gothwal
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Rajasthan, India
| | - Devendra Kumar Yadava
- Division of Crop Science, Indian Council of Agricultural Research (ICAR), New Delhi, India
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Ma X, Feng L, Tao A, Zenda T, He Y, Zhang D, Duan H, Tao Y. Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:259. [PMID: 38038768 DOI: 10.1007/s00122-023-04495-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023]
Abstract
KEY MESSAGE Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.
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Affiliation(s)
- Xiaolin Ma
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Liqing Feng
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Anyan Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Yuan He
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Daxiao Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| | - Yongsheng Tao
- State Key Laboratory of North China Crop Improvement and Regulation, North China Key Laboratory for Crop Germplasm Resources of the Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
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Li C, Dong S, Beckles DM, Liu X, Guan J, Gu X, Miao H, Zhang S. GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber. FRONTIERS IN PLANT SCIENCE 2023; 14:1116214. [PMID: 37235012 PMCID: PMC10208356 DOI: 10.3389/fpls.2023.1116214] [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: 12/05/2022] [Accepted: 03/24/2023] [Indexed: 05/28/2023]
Abstract
Low temperatures (LTs) negatively affect the percentage and rate of cucumber (Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: gLTG1.1, gLTG1.2, gLTG1.3, gLTG4.1, gLTG5.1, gLTG5.2, and gLTG6.1 after resequencing of the accessions. Of the seven loci, three, i.e., gLTG1.2, gLTG4.1, and gLTG5.2, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) for gLTG1.2, CsaV3_4G013480 (a RING-type E3 ubiquitin transferase) for gLTG4.1, and CsaV3_5G029350 (a serine/threonine-protein kinase) for gLTG5.2. The function for CsPPR (CsaV3_1G044080) in regulating LTG was confirmed, as Arabidopsis lines ectopically expressing CsPPR showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that CsPPR positively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.
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Affiliation(s)
- Caixia Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Diane M. Beckles
- Department of Plant Sciences, University of California Davis, Davis, CA, United States
| | - Xiaoping Liu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiantao Guan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
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Liang Z, Xi N, Liu H, Liu P, Xiang C, Zhang C, Zou C, Cheng X, Yu H, Zhang M, Chen Z, Pan G, Yuan G, Gao S, Ma L, Shen Y. An Integration of Linkage Mapping and GWAS Reveals the Key Genes for Ear Shank Length in Maize. Int J Mol Sci 2022; 23:ijms232315073. [PMID: 36499409 PMCID: PMC9740654 DOI: 10.3390/ijms232315073] [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: 10/15/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Ear shank length (ESL) has significant effects on grain yield and kernel dehydration rate in maize. Herein, linkage mapping and genome-wide association study were combined to reveal the genetic architecture of maize ESL. Sixteen quantitative trait loci (QTL) were identified in the segregation population, among which five were repeatedly detected across multiple environments. Meanwhile, 23 single nucleotide polymorphisms were associated with the ESL in the association panel, of which four were located in the QTL identified by linkage mapping and were designated as the population-common loci. A total of 42 genes residing in the linkage disequilibrium regions of these common variants and 12 of them were responsive to ear shank elongation. Of the 12 genes, five encode leucine-rich repeat receptor-like protein kinases, proline-rich proteins, and cyclin11, respectively, which were previously shown to regulate cell division, expansion, and elongation. Gene-based association analyses revealed that the variant located in Cyclin11 promoter affected the ESL among different lines. Cyclin11 showed the highest expression in the ear shank 15 days after silking among diverse tissues of maize, suggesting its role in modulating ESL. Our study contributes to the understanding of the genetic mechanism underlying maize ESL and genetic modification of maize dehydration rate and kernel yield.
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Genome-Wide Association Study Reveals the Genetic Basis of Kernel and Cob Moisture Changes in Maize at Physiological Maturity Stage. PLANTS 2022; 11:plants11151989. [PMID: 35956467 PMCID: PMC9370647 DOI: 10.3390/plants11151989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 07/24/2022] [Accepted: 07/28/2022] [Indexed: 11/17/2022]
Abstract
Low moisture content (MC) and high dehydration rate (DR) at physiological maturity affect grain mechanical harvest, transport, and storage. In this study, we used an association panel composed of 241 maize inbred lines to analyze ear moisture changes at physiological maturity stage. A genome-wide association study revealed nine significant SNPs and 91 candidate genes. One SNP (SYN38588) was repeatedly detected for two traits, and 15 candidate genes were scanned in the linkage disequilibrium regions of this SNP. Of these, genes Zm00001d020615 and Zm00001d020623 were individually annotated as a polygalacturonase (PG) and a copper transporter 5.1 (COPT5.1), respectively. Candidate gene association analysis showed that three SNPs located in the exons of Zm00001d020615 were significantly associated with the dehydration rate, and AATTAA was determined as the superior haplotype. All these findings suggested that Zm00001d020615 was a key gene affecting moisture changes of maize at the physiological maturity stage. These results have demonstrated the genetic basis of ear moisture changes in maize and indicated a superior haplotype for cultivating maize varieties with low moisture content and high dehydration rates.
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Ma L, Wang C, Hu Y, Dai W, Liang Z, Zou C, Pan G, Lübberstedt T, Shen Y. GWAS and transcriptome analysis reveal MADS26 involved in seed germination ability in maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1717-1730. [PMID: 35247071 DOI: 10.1007/s00122-022-04065-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/15/2022] [Indexed: 05/09/2023]
Abstract
MADS26 affecting maize seed germination was identified by GWAS and transcriptomics. Gene-based association analyses revealed three variations within MADS26 regulating seed germination traits. Overexpressed MADS26 in Arabidopsis improved seed germination. Seed germination ability is extremely important for maize production. Exploring the genetic control of seed germination ability is useful for improving maize yield. In this study, a genome-wide association study (GWAS) was conducted to excavate the significant SNPs involved in seed germination ability based on an association panel consisting of 300 lines. A total of 11 SNPs and 75 candidate genes were significantly associated with the seed germination traits. In addition, we constructed 24 transcriptome libraries from maize seeds at four germination stages using two inbred lines with contrasting germination rates. In total, 15,865 differentially expressed genes were induced during seed germination. Integrating the results of GWAS and transcriptome analysis uncovered four prioritized genes underlying maize seed germination. The variations located in the promoter of Zm00001d017932, a MADS-transcription factor 26 (MADS26), were verified to affect the seed germination, and the haplotype TAT was determined as a favorable haplotype for high-germination capability. MADS26 was induced to express by ethylene during seed germination in maize and overexpressing MADS26 increased the seed germination ability in Arabidopsis. These findings will contribute to understanding of the genetic and molecular mechanisms on seed germination and the genetic modification of seed germination ability in maize.
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Affiliation(s)
- Langlang Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chen Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Hu
- Zigong Research Institute of Agricultural Sciences, Zigong, 643002, China
| | - Wei Dai
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Zhenjuan Liang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangtang Pan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | | | - Yaou Shen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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Hou F, Liu K, Zhang N, Zou C, Yuan G, Gao S, Zhang M, Pan G, Ma L, Shen Y. Association mapping uncovers maize ZmbZIP107 regulating root system architecture and lead absorption under lead stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1015151. [PMID: 36226300 PMCID: PMC9549328 DOI: 10.3389/fpls.2022.1015151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/06/2022] [Indexed: 05/22/2023]
Abstract
Lead (Pb) is a highly toxic contaminant to living organisms and the environment. Excessive Pb in soils affects crop yield and quality, thus threatening human health via the food chain. Herein, we investigated Pb tolerance among a maize association panel using root bushiness (BSH) under Pb treatment as an indicator. Through a genome-wide association study of relative BSH, we identified four single nucleotide polymorphisms (SNPs) and 30 candidate genes associated with Pb tolerance in maize seedlings. Transcriptome analysis showed that four of the 30 genes were differentially responsive to Pb treatment between two maize lines with contrasting Pb tolerance. Among these, the ZmbZIP107 transcription factor was confirmed as the key gene controlling maize tolerance to Pb by using gene-based association studies. Two 5' UTR_variants in ZmbZIP107 affected its expression level and Pb tolerance among different maize lines. ZmbZIP107 protein was specifically targeted to the nucleus and ZmbZIP107 mRNA showed the highest expression in maize seedling roots among different tissues. Heterologous expression of ZmbZIP107 enhanced rice tolerance to Pb stress and decreased Pb absorption in the roots. Our study provided the basis for revelation of the molecular mechanism underlying Pb tolerance and contributed to cultivation of Pb-tolerant varieties in maize.
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Ma L, Zhang M, Chen J, Qing C, He S, Zou C, Yuan G, Yang C, Peng H, Pan G, Lübberstedt T, Shen Y. GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3305-3318. [PMID: 34218289 DOI: 10.1007/s00122-021-03897-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 06/25/2021] [Indexed: 05/20/2023]
Abstract
KEYMESSAGE Two hub genes GRMZM2G075104 and GRMZM2G333183 involved in salt tolerance were identified by GWAS and WGCNA. Furthermore, they were verified to affect salt tolerance by candidate gene association analysis. Salt stress influences maize growth and development. To decode the genetic basis and hub genes controlling salt tolerance is a meaningful exploration for cultivating salt-tolerant maize varieties. Herein, we used an association panel consisting of 305 lines to identify the genetic loci responsible for Na+- and K+-related traits in maize seedlings. Under the salt stress, seven significant single nucleotide polymorphisms were identified using a genome-wide association study, and 120 genes were obtained by scanning the linkage disequilibrium regions of these loci. According to the transcriptome data of the above 120 genes under salinity treatment, we conducted a weighted gene co-expression network analysis. Combined the gene annotations, two SNaC/SKC (shoot Na+ content/shoot K+ content)-associated genes GRMZM2G075104 and GRMZM2G333183 were finally identified as the hub genes involved in salt tolerance. Subsequently, these two genes were verified to affect salt tolerance of maize seedlings by candidate gene association analysis. Haplotypes TTGTCCG-CT and CTT were determined as favorable/salt-tolerance haplotypes for GRMZM2G075104 and GRMZM2G333183, respectively. These findings provide novel insights into genetic architectures underlying maize salt tolerance and contribute to the cultivation of salt-tolerant varieties in maize.
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Affiliation(s)
- Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Minyan Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jie Chen
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Chunyan Qing
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Shijiang He
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Guangsheng Yuan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Cong Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hua Peng
- Sichuan Tourism College, Chengdu, 610100, China
| | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | | | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
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11
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Li WX, Wang P, Zhao H, Sun X, Yang T, Li H, Hou Y, Liu C, Siyal M, Raja veesar R, Hu B, Ning H. QTL for Main Stem Node Number and Its Response to Plant Densities in 144 Soybean FW-RILs. FRONTIERS IN PLANT SCIENCE 2021; 12:666796. [PMID: 34489989 PMCID: PMC8417731 DOI: 10.3389/fpls.2021.666796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Although the main stem node number of soybean [Glycine max (L.) Merr. ] is an important yield-related trait, there have been limited studies on the effect of plant density on the identification of quantitative trait loci (QTL) for main stem node number (MSNN). To address this issue, here, 144 four-way recombinant inbred lines (FW-RILs) derived from Kenfeng 14, Kenfeng 15, Heinong 48, and Kenfeng 19 were used to identify QTL for MSNN with densities of 2.2 × 105 (D1) and 3 × 105 (D2) plants/ha in five environments by linkage and association studies. As a result, the linkage and association studies identified 40 and 28 QTL in D1 and D2, respectively, indicating the difference in QTL in various densities. Among these QTL, five were common in the two densities; 36 were singly identified for response to density; 12 were repeatedly identified by both response to density and phenotype of two densities. Thirty-one were repeatedly detected across various methods, densities, and environments in the linkage and association studies. Among the 24 common QTL in the linkage and association studies, 15 explained a phenotypic variation of more than 10%. Finally, Glyma.06G094400, Glyma.06G147600, Glyma.19G160800.1, and Glyma.19G161100 were predicted to be associated with MSNN. These findings will help to elucidate the genetic basis of MSNN and improve molecular assistant selection in high-yield soybean breeding.
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Affiliation(s)
- Wen-Xia Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Ping Wang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
- High Education Institute, Huaiyin Institute of Technology, Huai'an, China
| | - Hengxing Zhao
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Xu Sun
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Tao Yang
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Haoran Li
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Yongqin Hou
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Cuiqiao Liu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Mahfishan Siyal
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Rameez Raja veesar
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Bo Hu
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
| | - Hailong Ning
- Key Laboratory of Soybean Biology, Ministry of Education, Key Laboratory of Soybean Biology and Breeding/Genetics, Ministry of Agriculture, Northeast Agricultural University, Harbin, China
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12
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Zhang Y, Liu P, Wang C, Zhang N, Zhu Y, Zou C, Yuan G, Yang C, Gao S, Pan G, Ma L, Shen Y. Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize. PeerJ 2021; 9:e11707. [PMID: 34249517 PMCID: PMC8247712 DOI: 10.7717/peerj.11707] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P < 2.03 × 10-6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.
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Affiliation(s)
- Yinchao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peng Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chen Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Na Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuxiao Zhu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Chaoying Zou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangsheng Yuan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Cong Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guangtang Pan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Langlang Ma
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yaou Shen
- Maize Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
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