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Hu M, Tian H, Yang K, Ding S, Hao Y, Xu R, Zhang F, Liu H, Zhang D. Comprehensive Evaluation and Selection of 192 Maize Accessions from Different Sources. PLANTS (BASEL, SWITZERLAND) 2024; 13:1397. [PMID: 38794467 PMCID: PMC11125448 DOI: 10.3390/plants13101397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/15/2024] [Accepted: 05/02/2024] [Indexed: 05/26/2024]
Abstract
In the period 2022-2023, an analysis of fourteen phenotypic traits was conducted across 192 maize accessions in the Aral region of Xinjiang. The Shannon-Wiener diversity index was employed to quantify the phenotypic diversity among the accessions. Subsequently, a comprehensive evaluation of the index was performed utilizing correlation analysis, principal component analysis (PCA) and cluster analysis. The results highlighted significant findings: (1) A pronounced diversity was evident across the 192 maize accessions, accompanied by complex interrelationships among the traits. (2) The 14 phenotypic traits were transformed into 3 independent indicators through principal component analysis: spike factor, leaf width factor, and number of spikes per plant. (3) The 192 materials were divided into three groups using cluster analysis. The phenotypes in Group III exhibited the best performance, followed by those in Group I, and finally Group II. The selection of the three groups can vary depending on the breeding objectives. This study analysed the diversity of phenotypic traits in maize germplasm resources. Maize germplasm was categorised based on similar phenotypes. These findings provide theoretical insights for the study of maize accessions under analogous climatic conditions in Alar City, which lay the groundwork for the efficient utilization of existing germplasm as well as the development and selection of new varieties.
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Affiliation(s)
- Mengting Hu
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Huijuan Tian
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Kaizhi Yang
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Shuqi Ding
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Ying Hao
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Ruohang Xu
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Fulai Zhang
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Hong Liu
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
| | - Dan Zhang
- College of Agriculture, Tarim University, Alar 843300, China; (M.H.); (H.T.); (K.Y.); (S.D.); (Y.H.); (R.X.); (F.Z.); (H.L.)
- Key Laboratory of Genetic Improvement and Efficient Production for Specialty Crops in Arid Southern Xinjiang of Xinjiang Corps, Alar 843300, China
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Patel R, Memon J, Kumar S, Patel DA, Sakure AA, Patel MB, Das A, Karjagi CG, Patel S, Patel U, Roychowdhury R. Genetic Diversity and Population Structure of Maize ( Zea mays L.) Inbred Lines in Association with Phenotypic and Grain Qualitative Traits Using SSR Genotyping. PLANTS (BASEL, SWITZERLAND) 2024; 13:823. [PMID: 38592835 PMCID: PMC10975177 DOI: 10.3390/plants13060823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 02/26/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024]
Abstract
Maize (Zea mays L.) is an important cereal and is affected by climate change. Therefore, the production of climate-smart maize is urgently needed by preserving diverse genetic backgrounds through the exploration of their genetic diversity. To achieve this, 96 maize inbred lines were used to screen for phenotypic yield-associated traits and grain quality parameters. These traits were studied across two different environments (Anand and Godhra) and polymorphic simple sequence repeat (SSR) markers were employed to investigate the genetic diversity, population structure, and trait-linked association. Genotype-environment interaction (GEI) reveals that most of the phenotypic traits were governed by the genotype itself across the environments, except for plant and ear height, which largely interact with the environment. The genotypic correlation was found to be positive and significant among protein, lysine and tryptophan content. Similarly, yield-attributing traits like ear girth, kernel rows ear-1, kernels row-1 and number of kernels ear-1 were strongly correlated to each other. Pair-wise genetic distance ranged from 0.0983 (1820194/T1 and 1820192/4-20) to 0.7377 (IGI-1101 and 1820168/T1). The SSRs can discriminate the maize population into three distinct groups and shortlisted two genotypes (IGI-1101 and 1820168/T1) as highly diverse lines. Out of the studied 136 SSRs, 61 were polymorphic to amplify a total of 131 alleles (2-3 per loci) with 0.46 average gene diversity. The Polymorphism Information Content (PIC) ranged from 0.24 (umc1578) to 0.58 (umc2252). Similarly, population structure analysis revealed three distinct groups with 19.79% admixture among the genotypes. Genome-wide scanning through a mixed linear model identifies the stable association of the markers umc2038, umc2050 and umc2296 with protein, umc2296 and umc2252 with tryptophan, and umc1535 and umc1303 with total soluble sugar. The obtained maize lines and SSRs can be utilized in future maize breeding programs in relation to other trait characterizations, developments, and subsequent molecular breeding performances for trait introgression into elite genotypes.
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Affiliation(s)
- Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Juned Memon
- Department of Genetics and Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand 388110, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Dipak A. Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Manish B. Patel
- Main Maize Research Station, Anand Agricultural University, Godhra 389001, India
| | - Arna Das
- Department of Genetics and Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand 388110, India
| | | | - Swati Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand 388110, India
| | - Ujjaval Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari 396450, India
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)—Volcani Center, Rishon Lezion 7505101, Israel
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Sahito JH, Zhang H, Gishkori ZGN, Ma C, Wang Z, Ding D, Zhang X, Tang J. Advancements and Prospects of Genome-Wide Association Studies (GWAS) in Maize. Int J Mol Sci 2024; 25:1918. [PMID: 38339196 PMCID: PMC10855973 DOI: 10.3390/ijms25031918] [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: 12/04/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024] Open
Abstract
Genome-wide association studies (GWAS) have emerged as a powerful tool for unraveling intricate genotype-phenotype association across various species. Maize (Zea mays L.), renowned for its extensive genetic diversity and rapid linkage disequilibrium (LD), stands as an exemplary candidate for GWAS. In maize, GWAS has made significant advancements by pinpointing numerous genetic loci and potential genes associated with complex traits, including responses to both abiotic and biotic stress. These discoveries hold the promise of enhancing adaptability and yield through effective breeding strategies. Nevertheless, the impact of environmental stress on crop growth and yield is evident in various agronomic traits. Therefore, understanding the complex genetic basis of these traits becomes paramount. This review delves into current and future prospectives aimed at yield, quality, and environmental stress resilience in maize and also addresses the challenges encountered during genomic selection and molecular breeding, all facilitated by the utilization of GWAS. Furthermore, the integration of omics, including genomics, transcriptomics, proteomics, metabolomics, epigenomics, and phenomics has enriched our understanding of intricate traits in maize, thereby enhancing environmental stress tolerance and boosting maize production. Collectively, these insights not only advance our understanding of the genetic mechanism regulating complex traits but also propel the utilization of marker-assisted selection in maize molecular breeding programs, where GWAS plays a pivotal role. Therefore, GWAS provides robust support for delving into the genetic mechanism underlying complex traits in maize and enhancing breeding strategies.
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Affiliation(s)
- Javed Hussain Sahito
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Hao Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zeeshan Ghulam Nabi Gishkori
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Chenhui Ma
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhihao Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Dong Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Xuehai Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- The Shennong Laboratory, Zhengzhou 450002, China
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Zhang Z, Peng C, Xu W, Li Y, Qi X, Zhao M. Genome-wide association study of agronomic traits related to nitrogen use efficiency in Henan wheat. BMC Genomics 2024; 25:7. [PMID: 38166525 PMCID: PMC10759698 DOI: 10.1186/s12864-023-09922-0] [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: 07/14/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Nitrogen use efficiency (NUE) is closely related to crop yield and nitrogen fertilizer application rate. Although NUE is susceptible to environments, quantitative trait nucleotides (QTNs) for NUE in wheat germplasm populations have been rarely reported in genome-wide associated study. RESULTS In this study, 244 wheat accessions were phenotyped by three NUE-related traits in three environments and genotyped by 203,224 SNPs. All the phenotypes for each trait were used to associate with all the genotypes of these SNP markers for identifying QTNs and QTN-by-environment interactions via 3VmrMLM. Among 279 QTNs and one QTN-by-environment interaction for low nitrogen tolerance, 33 were stably identified, especially, one large QTN (r2 > 10%), qPHR3A.2, was newly identified for plant height ratio in one environment and multi-environment joint analysis. Among 52 genes around qPHR3A.2, four genes (TraesCS3A01G101900, TraesCS3A01G102200, TraesCS3A01G104100, and TraesCS3A01G105400) were found to be differentially expressed in low-nitrogen-tolerant wheat genotypes, while TaCLH2 (TraesCS3A01G101900) was putatively involved in porphyrin metabolism in KEGG enrichment analyses. CONCLUSIONS This study identified valuable candidate gene for low-N-tolerant wheat breeding and provides new insights into the genetic basis of low N tolerance in wheat.
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Affiliation(s)
- Zaicheng Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
| | - Chaojun Peng
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
| | - Weigang Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China.
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China.
| | - Yan Li
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
| | - Xueli Qi
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
| | - Mingzhong Zhao
- Institute of Crops Molecular Breeding, National Engineering Laboratory of Wheat, Key Laboratory of Wheat Biology and Genetic Breeding in Central Huanghuai Area, Ministry of Agriculture, Henan Key Laboratory of Wheat Germplasm Resources Innovation and Improvement, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, People's Republic of China
- The Shennong Laboratory, Zhengzhou, 450002, People's Republic of China
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