1
|
Li J, Yang M, He D, Luo Z, Li B, Huang X, Wu F, Xie G, Fan C, Sun W, Yu S, Wang L. Genome-wide association study of stem structural characteristics that extracted by a high-throughput phenotypic analysis "LabelmeP rice" in rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38860937 DOI: 10.1111/tpj.16872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/12/2024] [Accepted: 05/27/2024] [Indexed: 06/12/2024]
Abstract
Stem is important for assimilating transport and plant strength; however, less is known about the genetic basis of its structural characteristics. In this study, a high-throughput method, "LabelmeP rice" was developed to generate 14 traits related to stem regions and vascular bundles, which allows the establishment of a stem cross-section phenotype dataset containing anatomical information of 1738 images from hand-cut transections of stems collected from 387 rice germplasm accessions grown over two successive seasons. Then, the phenotypic diversity of the rice accessions was evaluated. Genome-wide association studies identified 94, 83, and 66 significant single nucleotide polymorphisms (SNPs) for the assayed traits in 2 years and their best linear unbiased estimates, respectively. These SNPs can be integrated into 29 quantitative trait loci (QTL), and 11 of them were common in 2 years, while correlated traits shared 19. In addition, 173 candidate genes were identified, and six located at significant SNPs were repeatedly detected and annotated with a potential function in stem development. By using three introgression lines (chromosome segment substitution lines), four of the 29 QTLs were validated. LOC_Os01g70200, located on the QTL uq1.4, is detected for the area of small vascular bundles (SVB) and the rate of large vascular bundles number to SVB number. Besides, the CRISPR/Cas9 editing approach has elucidated the function of the candidate gene LOC_Os06g46340 in stem development. In conclusion, the results present a time- and cost-effective method that provides convenience for extracting rice stem anatomical traits and the candidate genes/QTL, which would help improve rice.
Collapse
Affiliation(s)
- Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingchong Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Dandan He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Zixuan Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Bo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Xiaojin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
| | - Fangxi Wu
- Fujian Academy of Agricultural Sciences, Fujian, China
| | - Guosheng Xie
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chuchuan Fan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenqiang Sun
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sibin Yu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lingqiang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning, China
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
2
|
Xu L, Hao J, Lv M, Liu P, Ge Q, Zhang S, Yang J, Niu H, Wang Y, Xue Y, Lu X, Tang J, Zheng J, Gou M. A genome-wide association study identifies genes associated with cuticular wax metabolism in maize. PLANT PHYSIOLOGY 2024; 194:2616-2630. [PMID: 38206190 DOI: 10.1093/plphys/kiae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/20/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024]
Abstract
The plant cuticle is essential in plant defense against biotic and abiotic stresses. To systematically elucidate the genetic architecture of maize (Zea mays L.) cuticular wax metabolism, 2 cuticular wax-related traits, the chlorophyll extraction rate (CER) and water loss rate (WLR) of 389 maize inbred lines, were investigated and a genome-wide association study (GWAS) was performed using 1.25 million single nucleotide polymorphisms (SNPs). In total, 57 nonredundant quantitative trait loci (QTL) explaining 5.57% to 15.07% of the phenotypic variation for each QTL were identified. These QTLs contained 183 genes, among which 21 strong candidates were identified based on functional annotations and previous publications. Remarkably, 3 candidate genes that express differentially during cuticle development encode β-ketoacyl-CoA synthase (KCS). While ZmKCS19 was known to be involved in cuticle wax metabolism, ZmKCS12 and ZmKCS3 functions were not reported. The association between ZmKCS12 and WLR was confirmed by resequencing 106 inbred lines, and the variation of WLR was significant between different haplotypes of ZmKCS12. In this study, the loss-of-function mutant of ZmKCS12 exhibited wrinkled leaf morphology, altered wax crystal morphology, and decreased C32 wax monomer levels, causing an increased WLR and sensitivity to drought. These results confirm that ZmKCS12 plays a vital role in maize C32 wax monomer synthesis and is critical for drought tolerance. In sum, through GWAS of 2 cuticular wax-associated traits, this study reveals comprehensively the genetic architecture in maize cuticular wax metabolism and provides a valuable reference for the genetic improvement of stress tolerance in maize.
Collapse
Affiliation(s)
- Liping Xu
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Jiaxin Hao
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Mengfan Lv
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Peipei Liu
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Qidong Ge
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Sainan Zhang
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianping Yang
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Hongbin Niu
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Yiru Wang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yadong Xue
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoduo Lu
- Institute of Advanced Agricultural Technology, Qilu Normal University, Jinan 250200, China
| | - Jihua Tang
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| | - Jun Zheng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingyue Gou
- State Key Laboratory of Wheat and Maize Crops Science, Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
| |
Collapse
|
3
|
Duan H, Li J, Sun L, Xiong X, Xu S, Sun Y, Ju X, Xue Z, Gao J, Wang Y, Xie H, Ding D, Zhang X, Tang J. Identification of novel loci associated with starch content in maize kernels by a genome-wide association study using an enlarged SNP panel. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:91. [PMID: 38099287 PMCID: PMC10716104 DOI: 10.1007/s11032-023-01437-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
Starch is a major component of cereals, comprising over 70% of dry weight. It serves as a primary carbon source for humans and animals. In addition, starch is an indispensable industrial raw material. While maize (Zea mays) is a key crop and the primary source of starch, the genetic basis for starch content in maize kernels remains poorly understood. In this study, using an enlarged panel, we conducted a genome-wide association study (GWAS) based on best linear unbiased prediction (BLUP) value for starch content of 261 inbred lines across three environments. Compared with previous study, we identified 14 additional significant quantitative trait loci (QTL), encompassed a total of 42 genes, and indicated that increased marker density contributes to improved statistical power. By integrating gene expression profiling, Gene Ontology (GO) enrichment and haplotype analysis, several potential target genes that may play a role in regulating starch content in maize kernels have been identified. Notably, we found that ZmAPC4, associated with the significant SNP chr4.S_175584318, which encodes a WD40 repeat-like superfamily protein and is highly expressed in maize endosperm, might be a crucial regulator of maize kernel starch synthesis. Out of the 261 inbred lines analyzed, they were categorized into four haplotypes. Remarkably, it was observed that the inbred lines harboring hap4 demonstrated the highest starch content compared to the other haplotypes. Additionally, as a significant achievement, we have developed molecular markers that effectively differentiate maize inbred lines based on their starch content. Overall, our study provides valuable insights into the genetic basis of starch content and the molecular markers can be useful in breeding programs aimed at developing maize varieties with high starch content, thereby improving breeding efficiency. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01437-6.
Collapse
Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaolong Ju
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Zhengjie Xue
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yan Wang
- Zhucheng Mingjue Tender Company Limited, Weifang, China
| | - Huiling Xie
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Department of Agronomy, Henan Agricultural University, Agricultural Road No. 63, Zhengzhou, 450002 China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou, China
- The Shennong Laboratory, Zhengzhou, China
| |
Collapse
|
4
|
Wang J, Zhao S, Zhang Y, Lu X, Du J, Wang C, Wen W, Guo X, Zhao C. Investigating the genetic basis of maize ear characteristics: a comprehensive genome-wide study utilizing high-throughput phenotypic measurement method and system. FRONTIERS IN PLANT SCIENCE 2023; 14:1248446. [PMID: 37701799 PMCID: PMC10493325 DOI: 10.3389/fpls.2023.1248446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023]
Abstract
The morphology of maize ears plays a critical role in the breeding of new varieties and increasing yield. However, the study of traditional ear-related traits alone can no longer meet the requirements of breeding. In this study, 20 ear-related traits, including size, shape, number, and color, were obtained in 407 maize inbred lines at two sites using a high-throughput phenotypic measurement method and system. Significant correlations were found among these traits, particularly the novel trait ear shape (ES), which was correlated with traditional traits: kernel number per row and kernel number per ear. Pairwise comparison tests revealed that the inbred lines of tropical-subtropical were significantly different from other subpopulations in row numbers per ear, kernel numbers per ear, and ear color. A genome-wide association study identified 275, 434, and 362 Single nucleotide polymorphisms (SNPs) for Beijing, Sanya, and best linear unbiased prediction scenarios, respectively, explaining 3.78% to 24.17% of the phenotypic variance. Furthermore, 58 candidate genes with detailed functional descriptions common to more than two scenarios were discovered, with 40 genes being associated with color traits on chromosome 1. After analysis of haplotypes, gene expression, and annotated information, several candidate genes with high reliability were identified, including Zm00001d051328 for ear perimeter and width, zma-MIR159f for ear shape, Zm00001d053080 for kernel width and row number per ear, and Zm00001d048373 for the blue color channel of maize kernels in the red-green-blue color model. This study emphasizes the importance of researching novel phenotypic traits in maize by utilizing high-throughput phenotypic measurements. The identified genetic loci enrich the existing genetic studies related to maize ears.
Collapse
Affiliation(s)
- Jinglu Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shuaihao Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Ying Zhang
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xianju Lu
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianjun Du
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chuanyu Wang
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Weiliang Wen
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Xinyu Guo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Beijing Key Lab of Digital Plant, Information Technology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Chunjiang Zhao
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- National Engineering Research Center for Information Technology in Agriculture, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| |
Collapse
|
5
|
Duan H, Xue Z, Ju X, Yang L, Gao J, Sun L, Xu S, Li J, Xiong X, Sun Y, Wang Y, Zhang X, Ding D, Zhang X, Tang J. The genetic architecture of prolificacy in maize revealed by association mapping and bulk segregant analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:182. [PMID: 37555969 DOI: 10.1007/s00122-023-04434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 06/26/2023] [Indexed: 08/10/2023]
Abstract
KEY MESSAGE Here, we revealed maize prolificacy highly correlated with domestication and identified a causal gene ZmEN1 located in one novel QTL qGEN261 that regulating maize prolificacy by using multiple-mapping methods. The development of maize prolificacy (EN) is crucial for enhancing yield and breeding specialty varieties. To achieve this goal, we employed a genome-wide association study (GWAS) to analyze the genetic architecture of EN in maize. Using 492 inbred lines with a wide range of EN variability, our results demonstrated significant differences in genetic, environmental, and interaction effects. The broad-sense heritability (H2) of EN was 0.60. Through GWAS, we identified 527 significant single nucleotide polymorphisms (SNPs), involved 290 quantitative trait loci (QTL) and 806 genes. Of these SNPs, 18 and 509 were classified as major effect loci and minor loci, respectively. In addition, we performed a bulk segregant analysis (BSA) in an F2 population constructed by a few-ears line Zheng58 and a multi-ears line 647. Our BSA results identified one significant QTL, qBEN1. Importantly, combining the GWAS and BSA, four co-located QTL, involving six genes, were identified. Three of them were expressed in vegetative meristem, shoot tip, internode and tip of ear primordium, with ZmEN1, encodes an unknown auxin-like protein, having the highest expression level in these tissues. It suggested that ZmEN1 plays a crucial role in promoting axillary bud and tillering to encourage the formation of prolificacy. Haplotype analysis of ZmEN1 revealed significant differences between different haplotypes, with inbred lines carrying hap6 having more EN. Overall, this is the first report about using GWAS and BSA to dissect the genetic architecture of EN in maize, which can be valuable for breeding specialty maize varieties and improving maize yield.
Collapse
Affiliation(s)
- Haiyang Duan
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Zhengjie Xue
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xiaolong Ju
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Lu Yang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, People's Republic of China
| | - Jionghao Gao
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Li Sun
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Shuhao Xu
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Jianxin Li
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xuehang Xiong
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Yan Sun
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Yan Wang
- Zhucheng Mingjue Tender Company Limited, Weifang, People's Republic of China
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, People's Republic of China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China.
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, Department of Agronomy, College of Agronomy, Henan Agricultural University, No. 218 Ping'an Avenue, Zhengdong New District, Zhengzhou, 450046, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, People's Republic of China.
| |
Collapse
|
6
|
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.
Collapse
|