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Dong Y, Li G, Zhang X, Feng Z, Li T, Li Z, Xu S, Xu S, Liu W, Xue J. Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population. Int J Mol Sci 2024; 25:1190. [PMID: 38256265 PMCID: PMC10816832 DOI: 10.3390/ijms25021190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/14/2024] [Accepted: 01/16/2024] [Indexed: 01/24/2024] Open
Abstract
Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.
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Affiliation(s)
- Yuan Dong
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Guoliang Li
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing 100193, China
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Xinghua Zhang
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhiqian Feng
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Ting Li
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Zhoushuai Li
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Shutu Xu
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Wenxin Liu
- National Maize Improvement Center of China, Key Laboratory of Crop Heterosis and Utilization (MOE), China Agricultural University, Beijing 100193, China
| | - Jiquan Xue
- Key Laboratory of Biology and Genetic Breeding of Maize in Arid Area of Northwest Region, College of Agronomy, Northwest A&F University, Yangling 712100, China
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Qian F, Jing J, Zhang Z, Chen S, Sang Z, Li W. GWAS and Meta-QTL Analysis of Yield-Related Ear Traits in Maize. PLANTS (BASEL, SWITZERLAND) 2023; 12:3806. [PMID: 38005703 PMCID: PMC10674677 DOI: 10.3390/plants12223806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]
Abstract
Maize ear traits are an important component of yield, and the genetic basis of ear traits facilitates further yield improvement. In this study, a panel of 580 maize inbred lines were used as the study material, eight ear-related traits were measured through three years of planting, and whole genome sequencing was performed using the maize 40 K breeding chip based on genotyping by targeted sequencing (GBTS) technology. Five models were used to conduct a genome-wide association study (GWAS) on best linear unbiased estimate (BLUE) of ear traits to find the best model. The FarmCPU (Fixed and random model Circulating Probability Unification) model was the best model for this study; a total of 104 significant single nucleotide polymorphisms (SNPs) were detected, and 10 co-location SNPs were detected simultaneously in more than two environments. Through gene function annotation and prediction, a total of nine genes were identified as potentially associated with ear traits. Moreover, a total of 760 quantitative trait loci (QTL) associated with yield-related traits reported in 37 different articles were collected. Using the collected 760 QTL for meta-QTL analysis, a total of 41 MQTL (meta-QTL) associated with yield-related traits were identified, and 19 MQTL detected yield-related ear trait functional genes and candidate genes that have been reported in maize. Five significant SNPs detected by GWAS were located within these MQTL intervals, and another three significant SNPs were close to MQTL (less than 1 Mb). The results provide a theoretical reference for the analysis of the genetic basis of ear-related traits and the improvement of maize yield.
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Affiliation(s)
- Fu Qian
- Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China; (F.Q.); (Z.Z.); (S.C.)
- The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832003, China;
| | - Jianguo Jing
- The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832003, China;
| | - Zhanqin Zhang
- Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China; (F.Q.); (Z.Z.); (S.C.)
| | - Shubin Chen
- Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China; (F.Q.); (Z.Z.); (S.C.)
| | - Zhiqin Sang
- Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China; (F.Q.); (Z.Z.); (S.C.)
| | - Weihua Li
- The Key Laboratory of Oasis Eco-Agriculture, College of Agriculture, Shihezi University, Shihezi 832003, China;
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Dong Z, Wang Y, Bao J, Li Y, Yin Z, Long Y, Wan X. The Genetic Structures and Molecular Mechanisms Underlying Ear Traits in Maize ( Zea mays L.). Cells 2023; 12:1900. [PMID: 37508564 PMCID: PMC10378120 DOI: 10.3390/cells12141900] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
Maize (Zea mays L.) is one of the world's staple food crops. In order to feed the growing world population, improving maize yield is a top priority for breeding programs. Ear traits are important determinants of maize yield, and are mostly quantitatively inherited. To date, many studies relating to the genetic and molecular dissection of ear traits have been performed; therefore, we explored the genetic loci of the ear traits that were previously discovered in the genome-wide association study (GWAS) and quantitative trait locus (QTL) mapping studies, and refined 153 QTL and 85 quantitative trait nucleotide (QTN) clusters. Next, we shortlisted 19 common intervals (CIs) that can be detected simultaneously by both QTL mapping and GWAS, and 40 CIs that have pleiotropic effects on ear traits. Further, we predicted the best possible candidate genes from 71 QTL and 25 QTN clusters that could be valuable for maize yield improvement.
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Affiliation(s)
- Zhenying Dong
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Yanbo Wang
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Jianxi Bao
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Ya’nan Li
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Zechao Yin
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
| | - Yan Long
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xiangyuan Wan
- Research Institute of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China; (Z.D.)
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
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Jiang T, Zhang C, Zhang Z, Wen M, Qiu H. QTL mapping of maize ( Zea mays L.) kernel traits under low-phosphorus stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:435-445. [PMID: 37033769 PMCID: PMC10073376 DOI: 10.1007/s12298-023-01300-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 03/17/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Low-phosphorus stress significantly impacts the development of maize kernels. In this study, the phosphor efficient maize genotype 082 and phosphor deficient maize genotype Ye107, were used to construct an F2:3 population. QTL mapping was then employed to determine the genetic basis of differences in the maize kernel traits of the two parents in a low-phosphorus environment. This analysis revealed several major QTL that control environmental impacts on kernel length, width, thickness, and weight. These QTL were detected in all three environments and were distributed on five genome segments of chromosomes 3, 5, 6, and 9, and some new kernel-trait QTL were also detected (eg: Qkwid6, Qkthi3, Qkwei9, and Qklen3-1). These environmentally insensitive QTL can be stably expressed in low phosphorus environments, indicating that they can lay a foundation for the breeding of high phosphorus utilization efficiency germplasm. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01300-0.
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Affiliation(s)
- Tao Jiang
- College of Agriculture, Guizhou University, Guiyang, 550025 China
| | - Chenghua Zhang
- Shandong Academy of Agricultural Sciences, Jinan, 250100 China
| | - Zhi Zhang
- College of Agriculture, Guizhou University, Guiyang, 550025 China
| | - Min Wen
- Jilin Agricultural University, Changchun, 130118 China
| | - Hongbo Qiu
- College of Agriculture, Guizhou University, Guiyang, 550025 China
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Li R, Chen Z, Zheng R, Chen Q, Deng J, Li H, Huang J, Liang C, Shi T. QTL mapping and candidate gene analysis for yield and grain weight/size in Tartary buckwheat. BMC PLANT BIOLOGY 2023; 23:58. [PMID: 36703107 PMCID: PMC9878770 DOI: 10.1186/s12870-022-04004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Grain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary buckwheat. The identification of quantitative trait loci (QTLs)/genes for grain weight/size is an important objective of Tartary buckwheat genetic research and breeding programs. RESULTS Herein, we mapped the QTLs for GY, 1000-grain weight (TGW), grain length (GL), grain width (GW) and grain length-width ratio (L/W) in four environments using 221 recombinant inbred lines (XJ-RILs) derived from a cross of 'Xiaomiqiao × Jinqiaomai 2'. In total, 32 QTLs, including 7 for GY, 5 for TGW, 6 for GL, 11 for GW and 3 for L/W, were detected and distributed in 24 genomic regions. Two QTL clusters, qClu-1-3 and qClu-1-5, located on chromosome Ft1, were revealed to harbour 7 stable major QTLs for GY (qGY1.2), TGW (qTGW1.2), GL (qGL1.1 and qGL1.4), GW (qGW1.7 and qGW1.10) and L/W (qL/W1.2) repeatedly detected in three and above environments. A total of 59 homologues of 27 known plant grain weight/size genes were found within the physical intervals of qClu-1-3 and qClu-1-5. Six homologues, FtBRI1, FtAGB1, FtTGW6, FtMADS1, FtMKK4 and FtANT, were identified with both non-synonymous SNP/InDel variations and significantly differential expression levels between the two parents, which may play important roles in Tatary buckwheat grain weight/size control and were chosen as core candidate genes for further investigation. CONCLUSIONS Two stable major QTL clusters related to grain weight/size and six potential key candidate genes were identified by homology comparison, SNP/InDel variations and qRT‒qPCR analysis between the two parents. Our research provides valuable information for improving grain weight/size and yield in Tartary buckwheat breeding.
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Affiliation(s)
- Ruiyuan Li
- Key Laboratory of Information and Computing Science of Guizhou Province, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Zhengfeng Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Ran Zheng
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Jiao Deng
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Hongyou Li
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Juan Huang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Chenggang Liang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China.
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Wang C, Li H, Long Y, Dong Z, Wang J, Liu C, Wei X, Wan X. A Systemic Investigation of Genetic Architecture and Gene Resources Controlling Kernel Size-Related Traits in Maize. Int J Mol Sci 2023; 24:ijms24021025. [PMID: 36674545 PMCID: PMC9865405 DOI: 10.3390/ijms24021025] [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: 12/10/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023] Open
Abstract
Grain yield is the most critical and complex quantitative trait in maize. Kernel length (KL), kernel width (KW), kernel thickness (KT) and hundred-kernel weight (HKW) associated with kernel size are essential components of yield-related traits in maize. With the extensive use of quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) analyses, thousands of QTLs and quantitative trait nucleotides (QTNs) have been discovered for controlling these traits. However, only some of them have been cloned and successfully utilized in breeding programs. In this study, we exhaustively collected reported genes, QTLs and QTNs associated with the four traits, performed cluster identification of QTLs and QTNs, then combined QTL and QTN clusters to detect consensus hotspot regions. In total, 31 hotspots were identified for kernel size-related traits. Their candidate genes were predicted to be related to well-known pathways regulating the kernel developmental process. The identified hotspots can be further explored for fine mapping and candidate gene validation. Finally, we provided a strategy for high yield and quality maize. This study will not only facilitate causal genes cloning, but also guide the breeding practice for maize.
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Affiliation(s)
- Cheng Wang
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Huangai Li
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Yan Long
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Zhenying Dong
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Jianhui Wang
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Chang Liu
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
| | - Xun Wei
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
| | - Xiangyuan Wan
- Research Center of Biology and Agriculture, Shunde Innovation School, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 100083, China
- Beijing Engineering Laboratory of Main Crop Bio-Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio-Tech Breeding, Zhongzhi International Institute of Agricultural Biosciences, Beijing 100192, China
- Correspondence: (X.W.); (X.W.); Tel.: +86-189-1087-6260 (X.W.); +86-186-0056-1850 (X.W.)
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Genetic Architecture of Grain Yield-Related Traits in Sorghum and Maize. Int J Mol Sci 2022; 23:ijms23052405. [PMID: 35269548 PMCID: PMC8909957 DOI: 10.3390/ijms23052405] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/06/2022] [Accepted: 02/18/2022] [Indexed: 02/08/2023] Open
Abstract
Grain size, grain number per panicle, and grain weight are crucial determinants of yield-related traits in cereals. Understanding the genetic basis of grain yield-related traits has been the main research object and nodal in crop science. Sorghum and maize, as very close C4 crops with high photosynthetic rates, stress tolerance and large biomass characteristics, are extensively used to produce food, feed, and biofuels worldwide. In this review, we comprehensively summarize a large number of quantitative trait loci (QTLs) associated with grain yield in sorghum and maize. We placed great emphasis on discussing 22 fine-mapped QTLs and 30 functionally characterized genes, which greatly hinders our deep understanding at the molecular mechanism level. This review provides a general overview of the comprehensive findings on grain yield QTLs and discusses the emerging trend in molecular marker-assisted breeding with these QTLs.
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Qu X, Liu J, Xie X, Xu Q, Tang H, Mu Y, Pu Z, Li Y, Ma J, Gao Y, Jiang Q, Liu Y, Chen G, Wang J, Qi P, Habib A, Wei Y, Zheng Y, Lan X, Ma J. Genetic Mapping and Validation of Loci for Kernel-Related Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2021; 12:667493. [PMID: 34163507 PMCID: PMC8215603 DOI: 10.3389/fpls.2021.667493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/22/2021] [Indexed: 05/11/2023]
Abstract
Kernel size (KS) and kernel weight play a key role in wheat yield. Phenotypic data from six environments and a Wheat55K single-nucleotide polymorphism array-based constructed genetic linkage map from a recombinant inbred line population derived from the cross between the wheat line 20828 and the line SY95-71 were used to identify quantitative trait locus (QTL) for kernel length (KL), kernel width (KW), kernel thickness (KT), thousand-kernel weight (TKW), kernel length-width ratio (LWR), KS, and factor form density (FFD). The results showed that 65 QTLs associated with kernel traits were detected, of which the major QTLs QKL.sicau-2SY-1B, QKW.sicau-2SY-6D, QKT.sicau-2SY-2D, and QTKW.sicau-2SY-2D, QLWR.sicau-2SY-6D, QKS.sicau-2SY-1B/2D/6D, and QFFD.sicau-2SY-2D controlling KL, KW, KT, TKW, LWR, KS, and FFD, and identified in multiple environments, respectively. They were located on chromosomes 1BL, 2DL, and 6DS and formed three QTL clusters. Comparison of genetic and physical interval suggested that only QKL.sicau-2SY-1B located on chromosome 1BL was likely a novel QTL. A Kompetitive Allele Specific Polymerase chain reaction (KASP) marker, KASP-AX-109379070, closely linked to this novel QTL was developed and used to successfully confirm its effect in two different genetic populations and three variety panels consisting of 272 Chinese wheat landraces, 300 Chinese wheat cultivars most from the Yellow and Huai River Valley wheat region, and 165 Sichuan wheat cultivars. The relationships between kernel traits and other agronomic traits were detected and discussed. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified major QTL. Taken together, these stable and major QTLs provide valuable information for understanding the genetic composition of kernel yield and provide the basis for molecular marker-assisted breeding.
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Affiliation(s)
- Xiangru Qu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiajun Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xinlin Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yang Mu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhien Pu
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Yang Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yutian Gao
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ahsan Habib
- Biotechnology and Genetic Engineering Discipline, Khulna University, Khulna, Bangladesh
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Xiujin Lan,
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- Jian Ma, ;
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Mapping of QTL for Grain Yield Components Based on a DH Population in Maize. Sci Rep 2020; 10:7086. [PMID: 32341398 PMCID: PMC7184729 DOI: 10.1038/s41598-020-63960-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 04/08/2020] [Indexed: 11/27/2022] Open
Abstract
The elite maize hybrid Zhengdan 958 (ZD958), which has high and stable yield and extensive adaptability, is widely grown in China. To elucidate the genetic basis of yield and its related traits in this elite hybrid, a set of doubled haploid (DH) lines derived from ZD958 were evaluated in four different environments at two locations over two years, and a total of 49 quantitative trait loci (QTL) and 24 pairs of epistatic interactions related to yield and yield components were detected. Furthermore, 21 QTL for six investigated phenotypic traits were detected across two different sites. Combining the results of these QTL in each environment and across both sites, three main QTL hotspots were found in chromosomal bins 2.02, 2.05–2.06, and 6.05 between the simple sequence repeat (SSR) markers umc1165-bnlg1017, umc1065-umc1637, and nc012-bnlg345, respectively. The existence of three QTL hotspots associated with various traits across multiple environments could be explained by pleiotropic QTL or multiple tightly linked QTL. These genetic regions could provide targets for genetic improvement, fine mapping, and marker-assisted selection in future studies.
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10
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Liu M, Tan X, Yang Y, Liu P, Zhang X, Zhang Y, Wang L, Hu Y, Ma L, Li Z, Zhang Y, Zou C, Lin H, Gao S, Lee M, Lübberstedt T, Pan G, Shen Y. Analysis of the genetic architecture of maize kernel size traits by combined linkage and association mapping. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:207-221. [PMID: 31199064 PMCID: PMC6920160 DOI: 10.1111/pbi.13188] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 05/26/2019] [Accepted: 06/01/2019] [Indexed: 05/14/2023]
Abstract
Kernel size-related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P < 2.25 × 10-6 ) associated with these three traits in the association panel under four environments. Furthermore, 50 quantitative trait loci (QTL) controlling these traits were detected in seven environments in the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, of which eight were repetitively identified in at least three environments. Combining the two mapping populations revealed that 56 SNPs (P < 1 × 10-3 ) fell within 18 of the QTL confidence intervals. According to the top significant SNPs, stable-effect SNPs and the co-localized SNPs by association analysis and linkage mapping, a total of 73 candidate genes were identified, regulating seed development. Additionally, seven miRNAs were found to situate within the linkage disequilibrium (LD) regions of the co-localized SNPs, of which zma-miR164e was demonstrated to cleave the mRNAs of Arabidopsis CUC1, CUC2 and NAC6 in vitro. Overexpression of zma-miR164e resulted in the down-regulation of these genes above and the failure of seed formation in Arabidopsis pods, with the increased branch number. These findings provide insights into the mechanism of seed development and the improvement of molecular marker-assisted selection (MAS) for high-yield breeding in maize.
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Affiliation(s)
- Min Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiaolong Tan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yan Yang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Peng Liu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Xiaoxiang Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yinchao Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Lei Wang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yu Hu
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Langlang Ma
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Zhaoling Li
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yanling Zhang
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Chaoying Zou
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Haijian Lin
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Shibin Gao
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Michael Lee
- Department of AgronomyIowa State UniversityAmesIAUSA
| | | | - Guangtang Pan
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
| | - Yaou Shen
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest RegionMaize Research InstituteSichuan Agricultural UniversityChengduChina
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (In preparation)ChengduChina
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11
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Zhao X, Zhang J, Fang P, Peng Y. Comparative QTL analysis for yield components and morphological traits in maize ( Zea mays L.) under water-stressed and well-watered conditions. BREEDING SCIENCE 2019; 69:621-632. [PMID: 31988626 PMCID: PMC6977450 DOI: 10.1270/jsbbs.18021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 08/01/2019] [Indexed: 05/31/2023]
Abstract
Drought significantly influences maize morphology and yield potential. The elucidation of the genetic mechanisms of yield components and morphological traits, and tightly linked molecular markers under drought stress are thus of great importance in marker assisted selection (MAS) breeding. Here, we identified 32 QTLs for grain weight per ear, kernel ratio, and ear height-to-plant height ratio across two F2:3 populations under both drought and non-drought conditions by single-environment mapping with composite interval mapping (CIM), of which 21 QTLs were mapped under water-stressed conditions. We identified 29 QTLs by joint analysis of all environments with mixed-linear-model-based composite interval mapping (MCIM), 14 QTLs involved in QTL-by-environment interactions, and 11 epistatic interactions. Further analysis simultaneously identified 20 stable QTLs (sQTLs) by CIM and MCIM could be useful for genetic improvement of these traits via QTL pyramiding. Remarkably, bin 1.07-1.10/6.05/8.03/8.06 exhibited four pleiotropic sQTLs that were consistent with phenotypic correlations among traits, supporting the pleiotropy of QTLs and playing important roles in conferring growth and yield advantages under contrasting watering conditions. These findings provide information on the genetic mechanisms responsible for yield components and morphological traits that are affected by different watering conditions. Furthermore, these alleles provide useful targets for MAS.
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Affiliation(s)
- Xiaoqiang Zhao
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University,
Lanzhou 730070,
China
- College of Agronomy, Gansu Agricultural University,
Lanzhou 730070,
China
| | - Jinwen Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University,
Lanzhou 730070,
China
- College of Agronomy, Gansu Agricultural University,
Lanzhou 730070,
China
| | - Peng Fang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University,
Lanzhou 730070,
China
- College of Agronomy, Gansu Agricultural University,
Lanzhou 730070,
China
| | - Yunling Peng
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University,
Lanzhou 730070,
China
- College of Agronomy, Gansu Agricultural University,
Lanzhou 730070,
China
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12
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Identification of quantitative trait loci for kernel-related traits and the heterosis for these traits in maize (Zea mays L.). Mol Genet Genomics 2019; 295:121-133. [PMID: 31511973 DOI: 10.1007/s00438-019-01608-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/31/2019] [Indexed: 12/24/2022]
Abstract
Heterosis has been extensively applied for many traits during maize breeding, but there has been relatively little attention paid to the heterosis for kernel size. In this study, we evaluated a population of 301 recombinant inbred lines derived from a cross between 08-641 and YE478, as well as 298 hybrids from an immortalized F2 (IF2) population to detect quantitative trait loci (QTLs) for six kernel-related traits and the mid-parent heterosis (MPH) for these traits. A total of 100 QTLs, six pairs of loci with epistatic interactions, and five significant QTL × environment interactions were identified in both mapping populations. Seven QTLs accounted for over 10% of the phenotypic variation. Only four QTLs affected both the trait means and the MPH, suggesting the genetic mechanisms for kernel-related traits and the heterosis for kernel size are not completely independent. Moreover, more than half of the QTLs for each trait in the IF2 population exhibited dominance, implying that dominance is more important than other genetic effects for the heterosis for kernel-related traits. Additionally, 20 QTL clusters comprising 46 QTLs were detected across ten chromosomes. Specific chromosomal regions (bins 2.03, 6.04-6.05, and 9.01-9.02) exhibited pleiotropy and congruency across diverse heterotic patterns in previous studies. These results may provide additional insights into the genetic basis for the MPH for kernel-related traits.
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13
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Hao D, Xue L, Zhang Z, Cheng Y, Chen G, Zhou G, Li P, Yang Z, Xu C. Combined linkage and association mapping reveal candidate loci for kernel size and weight in maize. BREEDING SCIENCE 2019; 69:420-428. [PMID: 31598074 PMCID: PMC6776153 DOI: 10.1270/jsbbs.18185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/10/2019] [Indexed: 05/25/2023]
Abstract
Yield improvement is a top priority for maize breeding. Kernel size and weight are important determinants of maize grain yield. In this study, a recombinant inbred line (RIL) population and an association panel were used to identify quantitative trait loci (QTLs) for four maize kernel-related traits: kernel length, width, thickness and 100-kernel weight. Twenty-seven QTLs were identified for kernel-related traits across three environments and the best linear unbiased predictions (BLUPs) of each trait by linkage analysis, and four QTLs were stably detected in more than two environments. Additionally, 29 single nucleotide polymorphisms (SNPs) were identified as significantly associated with the four kernel-related traits and BLUPs by genome-wide association study, and two loci could be stably detected in both environments. In total, four QTLs/SNPs were co-associated with various traits in both populations. Using combined-linkage analysis and association mapping, PZE-101066560 on chromosome 1, associated with kernel width and with 100-kernel weight in the association panel, was co-localized within the QTL interval of qKW1-3 for kernel width in the RILs. Two annotated genes in the candidate region were considered as potential candidate genes. The QTLs and candidate genes identified here will facilitate molecular breeding for grain yield improvement in maize.
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Affiliation(s)
- Derong Hao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Lin Xue
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
- Jiangsu Collaborative Innovation Center for Modern Crop Production,
Nanjing 210095,
China
| | - Zhenliang Zhang
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Yujing Cheng
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Guoqing Chen
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
- Jiangsu Collaborative Innovation Center for Modern Crop Production,
Nanjing 210095,
China
| | - Guangfei Zhou
- Nantong Key Laboratory for Exploitation of Crop Genetic Resources and Molecular Breeding, Jiangsu Yanjiang Institute of Agricultural Sciences,
Nantong 226541,
China
| | - Pengcheng Li
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
| | - Chenwu Xu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University,
Yangzhou 225009,
China
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14
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Comparative mapping of quantitative trait loci for tassel-related traits of maize in $$\hbox {F}_{2:3}$$ F 2 : 3 and RIL populations. J Genet 2018. [DOI: 10.1007/s12041-018-0908-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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15
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Zhu XM, Shao XY, Pei YH, Guo XM, Li J, Song XY, Zhao MA. Genetic Diversity and Genome-Wide Association Study of Major Ear Quantitative Traits Using High-Density SNPs in Maize. FRONTIERS IN PLANT SCIENCE 2018; 9:966. [PMID: 30038634 PMCID: PMC6046616 DOI: 10.3389/fpls.2018.00966] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/15/2018] [Indexed: 05/21/2023]
Abstract
Kernel and ear traits are key components of grain yield in maize (Zea mays L.). Investigation of these traits would help to develop high-yield varieties in maize. Genome-wide association study (GWAS) uses the linkage disequilibrium (LD) in the whole genome to determine the genes affecting certain phenotype. In this study, five ear traits (kernel length and width, ear length and diameter, cob diameter) were investigated across multi-environments for 2 years. Combining with the genotype obtained from Maize SNP50 chip, genetic diversity and association mapping in a set of 292 inbred lines were performed. Results showed that maize lines were clustered into seven subgroups and a total of 20 SNPs were found to be associated with ear traits significantly (P < 3.95E-05). The candidate genes identified by GWAS mainly encoded ubiquitin-activation enzymes (GRMZM2G015287), carotenoid cleavage dioxygenase (GRMZM2G446858), MYB-CC type transfactor, and phosphate starvation response protein 3, and they were associated with kernel length (KL) and ear diameter (ED), respectively. Moreover, two novel genes corresponding to RNA processing and fructose metabolism were found. Further, the SNPs detected by GWAS were confirmed by meta-QTL analysis. These genes and SNPs identified in the study would offer essential information for yield-related genes clone and breeding program in maize.
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Affiliation(s)
- Xiao-Mei Zhu
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xiao-Yu Shao
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Yu-He Pei
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, China
| | - Xin-Mei Guo
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, China
| | - Jun Li
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, China
| | - Xi-Yun Song
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, China
- *Correspondence: Mei-Ai Zhao Xi-Yun Song,
| | - Mei-Ai Zhao
- Key Lab of Plant Biotechnology in Universities of Shandong Province, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Qingdao Major Crop Germplasm Resource Innovation and Application, Qingdao, China
- *Correspondence: Mei-Ai Zhao Xi-Yun Song,
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16
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Zhang C, Zhou Z, Yong H, Zhang X, Hao Z, Zhang F, Li M, Zhang D, Li X, Wang Z, Weng J. Analysis of the genetic architecture of maize ear and grain morphological traits by combined linkage and association mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1011-1029. [PMID: 28215025 DOI: 10.1007/s00122-017-2867-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 01/24/2017] [Indexed: 05/05/2023]
Abstract
Using combined linkage and association mapping, 26 stable QTL and six stable SNPs were detected across multiple environments for eight ear and grain morphological traits in maize. One QTL, PKS2, might play an important role in maize yield improvement. In the present study, one bi-parental population and an association panel were used to identify quantitative trait loci (QTL) for eight ear and grain morphological traits. A total of 108 QTL related to these traits were detected across four environments using an ultra-high density bin map constructed using recombinant inbred lines (RILs) derived from a cross between Ye478 and Qi319, and 26 QTL were identified in more than two environments. Furthermore, 64 single nucleotide polymorphisms (SNPs) were found to be significantly associated with the eight ear and grain morphological traits (-log10(P) > 4) in an association panel of 240 maize inbred lines. Combining the two mapping populations, a total of 17 pleiotropic QTL/SNPs (pQTL/SNPs) were associated with various traits across multiple environments. PKS2, a stable locus influencing kernel shape identified on chromosome 2 in a genome-wide association study (GWAS), was within the QTL confidence interval defined by the RILs. The candidate region harbored a short 13-Kb LD block encompassing four SNPs (SYN11386, PHM14783.16, SYN11392, and SYN11378). In the association panel, 13 lines derived from the hybrid PI78599 possessed the same allele as Qi319 at the PHM14783.16 (GG) locus, with an average value of 0.21 for KS, significantly lower than that of the 34 lines derived from Ye478 that carried a different allele (0.25, P < 0.05). Therefore, further fine mapping of PKS2 will provide valuable information for understanding the genetic components of grain yield and improving molecular marker-assisted selection (MAS) in maize.
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Affiliation(s)
- Chaoshu Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Zhiqiang Zhou
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Hongjun Yong
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Xiaochong Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Zhuanfang Hao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Fangjun Zhang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Mingshun Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Degui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Xinhai Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China
| | - Zhenhua Wang
- College of Agronomy, Northeast Agricultural University, Mucai Street, XiangFang District, Harbin, 150030, Heilongjiang, China.
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing, 100081, China.
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