1
|
Wang J, Li C, Li L, Gao L, Hu G, Zhang Y, Reynolds MP, Zhang X, Jia J, Mao X, Jing R. DIW1 encoding a clade I PP2C phosphatase negatively regulates drought tolerance by de-phosphorylating TaSnRK1.1 in wheat. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1918-1936. [PMID: 37158049 DOI: 10.1111/jipb.13504] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/05/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
Drought seriously impacts wheat production (Triticum aestivum L.), while the exploitation and utilization of genes for drought tolerance are insufficient. Leaf wilting is a direct reflection of drought tolerance in plants. Clade A PP2Cs are abscisic acid (ABA) co-receptors playing vital roles in the ABA signaling pathway, regulating drought response. However, the roles of other clade PP2Cs in drought tolerance, especially in wheat, remain largely unknown. Here, we identified a gain-of-function drought-induced wilting 1 (DIW1) gene from the wheat Aikang 58 mutant library by map-based cloning, which encodes a clade I protein phosphatase 2C (TaPP2C158) with enhanced protein phosphatase activity. Phenotypic analysis of overexpression and CRISPR/Cas9 mutant lines demonstrated that DIW1/TaPP2C158 is a negative regulator responsible for drought resistance. We found that TaPP2C158 directly interacts with TaSnRK1.1 and de-phosphorylates it, thus inactivating the TaSnRK1.1-TaAREB3 pathway. TaPP2C158 protein phosphatase activity is negatively correlated with ABA signaling. Association analysis suggested that C-terminal variation of TaPP2C158 changing protein phosphatase activity is highly correlated with the canopy temperature, and seedling survival rate under drought stress. Our data suggest that the favorable allele with lower phosphatase activity of TaPP2C158 has been positively selected in Chinese breeding history. This work benefits us in understanding the molecular mechanism of wheat drought tolerance, and provides elite genetic resources and molecular markers for improving wheat drought tolerance.
Collapse
Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ge Hu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yanfei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Matthew P Reynolds
- International Maize and Wheat Improvement Center, Texcoco, 56237, Mexico
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
2
|
Türkoğlu A, Haliloğlu K, Mohammadi SA, Öztürk A, Bolouri P, Özkan G, Bocianowski J, Pour-Aboughadareh A, Jamshidi B. Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats (SSR) Markers. Genes (Basel) 2023; 14:1182. [PMID: 37372362 DOI: 10.3390/genes14061182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses.
Collapse
Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, 42310 Konya, Turkey
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Seyyed Abolgahasem Mohammadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz 5166616471, Iran
| | - Ali Öztürk
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Parisa Bolouri
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, 06100 Ankara, Turkey
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31585-854, Iran
| | - Bita Jamshidi
- Department of Food Security and Public Health, Khabat Technical Institute, Erbil Polytechnic University, Erbil 44001, Iraq
| |
Collapse
|
3
|
Wang X, Liu Y, Hao C, Li T, Majeed U, Liu H, Li H, Hou J, Zhang X. Wheat NAC-A18 regulates grain starch and storage proteins synthesis and affects grain weight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:123. [PMID: 37147554 DOI: 10.1007/s00122-023-04365-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 04/14/2023] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Wheat NAC-A18 regulates both starch and storage protein synthesis in the grain, and a haplotype with positive effects on grain weight showed increased frequency during wheat breeding in China. Starch and seed storage protein (SSP) directly affect the processing quality of wheat grain. The synthesis of starch and SSP are also regulated at the transcriptional level. However, only a few starch and SSP regulators have been identified in wheat. In this study, we discovered a NAC transcription factor, designated as NAC-A18, which acts as a regulator of both starch and SSP synthesis. NAC-A18, is predominately expressed in wheat developing grains, encodes a transcription factor localized in the nucleus, with both activation and repression domains. Ectopic expression of wheat NAC-A18 in rice significantly decreased starch accumulation and increased SSP accumulation and grain size and weight. Dual-luciferase reporter assays indicated that NAC-A18 could reduce the expression of TaGBSSI-A1 and TaGBSSI-A2, and enhance the expression of TaLMW-D6 and TaLMW-D1. A yeast one hybrid assay demonstrated that NAC-A18 bound directly to the cis-element "ACGCAA" in the promoters of TaLMW-D6 and TaLMW-D1. Further analysis indicated that two haplotypes were formed at NAC-A18, and that NAC-A18_h1 was a favorable haplotype correlated with higher thousand grain weight. Based on limited population data, NAC-A18_h1 underwent positive selection during Chinese wheat breeding. Our study demonstrates that wheat NAC-A18 regulates starch and SSP accumulation and grain size. A molecular marker was developed for the favorable allele for breeding applications.
Collapse
Affiliation(s)
- Xiaolu Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunchuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Uzma Majeed
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huifang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
4
|
Dong C, Zhang L, Zhang Q, Yang Y, Li D, Xie Z, Cui G, Chen Y, Wu L, Li Z, Liu G, Zhang X, Liu C, Chu J, Zhao G, Xia C, Jia J, Sun J, Kong X, Liu X. Tiller Number1 encodes an ankyrin repeat protein that controls tillering in bread wheat. Nat Commun 2023; 14:836. [PMID: 36788238 PMCID: PMC9929037 DOI: 10.1038/s41467-023-36271-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 01/23/2023] [Indexed: 02/16/2023] Open
Abstract
Wheat (Triticum aestivum L.) is a major staple food for more than one-third of the world's population. Tiller number is an important agronomic trait in wheat, but only few related genes have been cloned. Here, we isolate a wheat mutant, tiller number1 (tn1), with much fewer tillers. We clone the TN1 gene via map-based cloning: TN1 encodes an ankyrin repeat protein with a transmembrane domain (ANK-TM). We show that a single amino acid substitution in the third conserved ankyrin repeat domain causes the decreased tiller number of tn1 mutant plants. Resequencing and haplotype analysis indicate that TN1 is conserved in wheat landraces and modern cultivars. Further, we reveal that the expression level of the abscisic acid (ABA) biosynthetic gene TaNCED3 and ABA content are significantly increased in the shoot base and tiller bud of the tn1 mutants; TN1 but not tn1 could inhibit the binding of TaPYL to TaPP2C via direct interaction with TaPYL. Taken together, we clone a key wheat tiller number regulatory gene TN1, which promotes tiller bud outgrowth probably through inhibiting ABA biosynthesis and signaling.
Collapse
Affiliation(s)
- Chunhao Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lichao Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qiang Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,State Key Lab of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Yuxin Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Danping Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhencheng Xie
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoqing Cui
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yaoyu Chen
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lifen Wu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhan Li
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Guoxiang Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueying Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Cuimei Liu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Innovation Academy for Seed Design, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guangyao Zhao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chuan Xia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jizeng Jia
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xiuying Kong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| |
Collapse
|
5
|
Genetic Diversity and Population Structure Analysis of Castanopsis hystrix and Construction of a Core Collection Using Phenotypic Traits and Molecular Markers. Genes (Basel) 2022; 13:genes13122383. [PMID: 36553650 PMCID: PMC9778198 DOI: 10.3390/genes13122383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/20/2022] [Accepted: 12/05/2022] [Indexed: 12/23/2022] Open
Abstract
Castanopsis hystrix is a valuable native, broad-leaved, and fast-growing tree in South China. In this study, 15 phenotypic traits and 32 simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of a natural population of C. hystrix and to construct a core germplasm collection by a set of 232 accessions. The results showed that the original population of C. hystrix had relatively high genetic diversity, with the number of alleles (Na), effective number of alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), Shannon's information index (I), and polymorphism information content (PIC) averaging at 26.188, 11.565, 0.863, 0.897, 2.660, and 0.889, respectively. Three sub-populations were identified based on a STRUCTURE analysis, indicating a strong genetic structure. The results from the phylogenetic and population structures showed a high level of agreement, with 232 germplasms being classified into three main groups. The analysis of molecular variance (AMOVA) test indicated that 96% of the total variance was derived from within populations, which revealed a low differentiation among populations. A core collection composed of 157 germplasms was firstly constructed thereafter, of which the diversity parameters non-significantly differed from the original population. These results revealed the genetic diversity and population structure of C. hystrix germplasms, which have implications for germplasm management and genome-wide association studies on C. hystrix, as well as for core collection establishment applications in other wood-producing hardwood species.
Collapse
|
6
|
Khan N, Zhang Y, Wang J, Li Y, Chen X, Yang L, Zhang J, Li C, Li L, Ur Rehman S, Reynolds MP, Zhang L, Zhang X, Mao X, Jing R. TaGSNE, a WRKY transcription factor, overcomes the trade-off between grain size and grain number in common wheat and is associated with root development. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6678-6696. [PMID: 35906966 DOI: 10.1093/jxb/erac327] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 07/26/2022] [Indexed: 05/28/2023]
Abstract
Wheat is one of the world's major staple food crops, and breeding for improvement of grain yield is a priority under the scenarios of climate change and population growth. WRKY transcription factors are multifaceted regulators in plant growth, development, and responses to environmental stimuli. In this study, we identify the WRKY gene TaGSNE (Grain Size and Number Enhancer) in common wheat, and find that it has relatively high expression in leaves and roots, and is induced by multiple abiotic stresses. Eleven single-nucleotide polymorphisms were identified in TaGSNE, forming two haplotypes in multiple germplasm collections, named as TaGSNE-Hap-1 and TaGSNE-Hap-2. In a range of different environments, TaGSNE-Hap-2 was significantly associated with increases in thousand-grain weight (TGW; 3.0%) and spikelet number per spike (4.1%), as well as with deeper roots (10.1%) and increased root dry weight (8.3%) at the mid-grain-filling stage, and these were confirmed in backcross introgression populations. Furthermore, transgenic rice lines overexpressing TaGSNE had larger panicles, more grains, increased grain size, and increased grain yield relative to the wild-type control. Analysis of geographic and temporal distributions revealed that TaGSNE-Hap-2 is positively selected in China and Pakistan, and TaGSNE-Hap-1 in Europe. Our findings demonstrate that TaGSNE overcomes the trade-off between TGW/grain size and grain number, leading us to conclude that these elite haplotypes and their functional markers could be utilized in marker-assisted selection for breeding high-yielding varieties.
Collapse
Affiliation(s)
- Nadia Khan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Genetics, University of Karachi, Pakistan
| | - Yanfei Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuying Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xin Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lili Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shoaib Ur Rehman
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan 60000, Pakistan
| | | | - Lichao Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
7
|
Zheng J, Wang X, Wu B, Qiao L, Zhao J, Pourkheirandish M, Wang J, Zheng X. Folate (vitamin B9) content analysis in bread wheat (Triticum aestivum L.). Front Nutr 2022; 9:933358. [PMID: 36337661 PMCID: PMC9633958 DOI: 10.3389/fnut.2022.933358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
Vitamin B9, particularly folic acid, is an essential molecule for human health. Wheat flour is one of the major sources of calorie intake by humans. The selection of folate-rich genotypes in wheat breeding can enhance the natural folate value in the daily diet. This study used a precise, high-performance liquid chromatography (HPLC) assay to analyze folate content in a 262-accession Chinese wheat mini-core collection (MCC) grown under three environments. Four folate derivatives in grains including tetrahydrofolate (THF), 5-methyltetrahydrofolate (5-CH3-THF), 5-formyltetrahydrofolate (5-CHO-THF), and 5,10-methenyltetrahydrofolate (5,10-CH+THF) were considered. An association analysis of water regimes, accession types, released years, geographical origin, and agronomic traits with folate content was conducted for the first time. There was a large amount of variation in folate content in the analyzed accessions, with genotype identified as the main influencing factor. Total folate content was significantly correlated with the content of the four MCC derivatives under the three environments. 5-CH3-THF and 5-CHO-THF were the most abundant among the four folate derivatives and were positively correlated with high folate content. The 12 accessions with the highest folate content showed an average of more than 80 μg/100 g. The analysis demonstrated that this Chinese wheat had not undergone extensive selection for folate content during breeding, which is unrelated to the geographical origin, accession types, winter/spring types, and grain colors of wheat. The content of THF, 5-CH3-THF, and 5,10-CH+THF was significantly negatively correlated with grain width, grain thickness, and thousand kernel weight. A relatively weak negative relationship manifested between folate contents and flowering date, whereas no significant correlation with tiller number, grain number per spike, maturity date, height, and spike length was detected. The investigation benefits wheat breeders for folate enhancement.
Collapse
Affiliation(s)
- Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Xingsu Wang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, Australia
- Mohammad Pourkheirandish,
| | - Juanling Wang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- Juanling Wang,
| | - Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
- *Correspondence: Xingwei Zheng,
| |
Collapse
|
8
|
Li XH, Guan PF, Huang S, Zheng XW, Wu BB, Zhao JJ, Qiao L, Guo PY, Zheng J. Evaluation and genetic variation of lutein content in Chinese common wheat. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
9
|
Li J, Zhou K, Wang Z, Zhou J, Deng X. 基于隐性核雄性不育系的杂交小麦制种技术研究进展、问题与展望. CHINESE SCIENCE BULLETIN-CHINESE 2022. [DOI: 10.1360/tb-2022-0386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
10
|
Building a Calibration Set for Genomic Prediction, Characteristics to Be Considered, and Optimization Approaches. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2467:77-112. [PMID: 35451773 DOI: 10.1007/978-1-0716-2205-6_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The efficiency of genomic selection strongly depends on the prediction accuracy of the genetic merit of candidates. Numerous papers have shown that the composition of the calibration set is a key contributor to prediction accuracy. A poorly defined calibration set can result in low accuracies, whereas an optimized one can considerably increase accuracy compared to random sampling, for a same size. Alternatively, optimizing the calibration set can be a way of decreasing the costs of phenotyping by enabling similar levels of accuracy compared to random sampling but with fewer phenotypic units. We present here the different factors that have to be considered when designing a calibration set, and review the different criteria proposed in the literature. We classified these criteria into two groups: model-free criteria based on relatedness, and criteria derived from the linear mixed model. We introduce criteria targeting specific prediction objectives including the prediction of highly diverse panels, biparental families, or hybrids. We also review different ways of updating the calibration set, and different procedures for optimizing phenotyping experimental designs.
Collapse
|
11
|
Zheng X, Qiao L, Liu Y, Wei N, Zhao J, Wu B, Yang B, Wang J, Zheng J. Genome-Wide Association Study of Grain Number in Common Wheat From Shanxi Under Different Water Regimes. FRONTIERS IN PLANT SCIENCE 2022; 12:806295. [PMID: 35154198 PMCID: PMC8825475 DOI: 10.3389/fpls.2021.806295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
Water availability is a crucial environmental factor on grain number in wheat, which is one of the important yield-related traits. In this study, a diverse panel of 282 wheat accessions were phenotyped for grain number per spike (GNS), spikelet number (SN), basal sterile spikelet number (BSSN), and apical sterile spikelet number (ASSN) under different water regimes across two growing seasons. Correlation analysis showed that GNS is significantly correlated with both SN and BSSN under two water regimes. A total of 9,793 single nucleotide polymorphism (SNP) markers from the 15 K wheat array were employed for genome-wide association study (GWAS). A total of 77 significant marker-trait associations (MTAs) for investigated traits as well as 8 MTAs for drought tolerance coefficient (DTC) were identified using the mixed linear model. Favored alleles for breeding were inferred according to their estimated effects on GNS, based on the mean difference of varieties. Frequency changes in favored alleles associated with GNS in modern varieties indicate there is still considerable genetic potential for their use as markers for genome selection of GNS in wheat breeding.
Collapse
Affiliation(s)
- Xingwei Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ling Qiao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ye Liu
- College of Life Science, Shanxi University, Taiyuan, China
| | - Naicui Wei
- College of Life Science, Shanxi University, Taiyuan, China
| | - Jiajia Zhao
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bangbang Wu
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Bin Yang
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Juanling Wang
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- State Key Laboratory of Sustainable Dryland Agriculture, Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| |
Collapse
|
12
|
Khan A, Ahmad M, Ahmed M, Gill KS, Akram Z. Association analysis for agronomic traits in wheat under terminal heat stress. Saudi J Biol Sci 2021; 28:7404-7415. [PMID: 34867044 PMCID: PMC8626334 DOI: 10.1016/j.sjbs.2021.08.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 12/01/2022] Open
Abstract
Terminal heat stress leads to irreversible damage in wheat. Marker assisted selection and gene pyramiding for portrayal of heat tolerance. Allelic frequency and polymorphic information showed significant variability. Markers xcfa2147 and xwmc671 could be potentail for heat stress tolerance.
Terminal heat stress causes irreversible damage to wheat crop productivity. It reduces the vegetative growth and flowering period that consequently declines the efficiency to capture available stem reserves (carbohydrates) in grains. Markers associated with thermotolerant traits ease in marker assisted selection (MAS) for crop improvement. It identifies the genomic regions associated with thermotolerant traits in wheat, but the scarcity of markers is the major hindrance in crop improvement. Therefore, 158 wheat genotypes were subjected to genotyping with 165 simple sequence repeat markers dispersed on three genomes (A, B and D). Allelic frequency and polymorphic information content values were highest on genome A (5.34 (14% greater than the lowest value at genome D) and 0.715 (3% greater than the lowest value at genome D)), chromosome 4 (5.40 (16% greater than the lowest value at chromosome 2) and 0.725 (5% greater than the lowest value at chromosome 6)) and marker xgwm44 (13.0 (84% greater than the lowest value at marker xbarc148) and 0.916 (46% greater than the lowest value at marker xbarc148)). Bayesian based population structure discriminated the wheat genotypes into seven groups based on genetic similarity indicating their ancestral origin and geographical ecotype. Linkage disequilibrium pattern had highest significant (P < 0.001) linked loci pairs 732 on genome A at r2 > 0.1 whereas, 58 on genome B at r2 > 0.5. Linkage disequilibrium decay (P < 0.01 and r2 > 0.1) had larger LD block (5–10 cM) on genome A. Highly significant MTAs (P < 0.000061) under heat stress conditions were identified for flag leaf area (xwmc336), spikelet per spike (xwmc553), grains per spike (cxfa2147, xwmc418 and xwmc121), biomass (xbarc7) and grain yield (xcfa2147 and xwmc671). The identified markers in this study could facilitate in MAS and gene pyramiding against heat stress in wheat.
Collapse
Affiliation(s)
- Adeel Khan
- Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Munir Ahmad
- Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Mukhtar Ahmed
- Department of Agronomy, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan.,Department of Agricultural Research for Northern Sweden, Swedish University of Agricultural Sciences, 90183 UMEÅ, Sweden
| | - Kulvinder Singh Gill
- Department of Crop and Soil Sciences, Washington State University, Pullman 646420, USA
| | - Zahid Akram
- Department of Plant Breeding and Genetics, PMAS-Arid Agriculture University, Rawalpindi 46300, Pakistan
| |
Collapse
|
13
|
Volante A, Barabaschi D, Marino R, Brandolini A. Genome-wide association study for morphological, phenological, quality, and yield traits in einkorn (Triticum monococcum L. subsp. monococcum). G3 (BETHESDA, MD.) 2021; 11:jkab281. [PMID: 34849796 PMCID: PMC8527505 DOI: 10.1093/g3journal/jkab281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 07/27/2021] [Indexed: 11/12/2022]
Abstract
Einkorn (Triticum monococcum L. subsp. monococcum, 2n = 2× = 14, AmAm) is a diploid wheat whose cultivation was widespread in the Mediterranean and European area till the Bronze Age, before it was replaced by the more productive durum and bread wheats. Although scarcely cultivated nowadays, it has gained renewed interest due to its relevant nutritional properties and as source of genetic diversity for crop breeding. However, the molecular basis of many traits of interest in einkorn remain still unknown. A panel of 160 einkorn landraces, from different parts of the distribution area, was characterized for several phenotypic traits related to morphology, phenology, quality, and yield for 4 years in two locations. An approach based on co-linearity with the A genome of bread wheat, supported also by that with Triticum urartu genome, was exploited to perform association mapping, even without an einkorn anchored genome. The association mapping approach uncovered numerous marker-trait associations; for 37 of these, a physical position was inferred by homology with the bread wheat genome. Moreover, numerous associated regions were also assigned to the available T. monococcum contigs. Among the intervals detected in this work, three overlapped with regions previously described as involved in the same trait, while four other regions were localized in proximity of loci previously described and presumably refer to the same gene/QTL. The remaining associated regions identified in this work could represent a novel and useful starting point for breeding approaches to improve the investigated traits in this neglected species.
Collapse
Affiliation(s)
- Andrea Volante
- CREA—Research Centre for Cereal and Industrial Crops, 13100 Vercelli, Italy
| | - Delfina Barabaschi
- CREA—Research Centre for Genomics and Bioinformatics, 29017 Fiorenzuola d’Arda, Italy and
| | - Rosanna Marino
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
| | - Andrea Brandolini
- CREA—Research Centre for Animal Production and Aquaculture, 26900 Lodi, Italy
| |
Collapse
|
14
|
Xue Y, Wang J, Mao X, Li C, Li L, Yang X, Hao C, Chang X, Li R, Jing R. Association Analysis Revealed That TaPYL4 Genes Are Linked to Plant Growth Related Traits in Multiple Environment. FRONTIERS IN PLANT SCIENCE 2021; 12:641087. [PMID: 34456932 PMCID: PMC8387097 DOI: 10.3389/fpls.2021.641087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Abscisic acid (ABA), one of phytohormones, plays an important regulatory role in plant growth and development. ABA receptor PYL4 (pyrabactin resistance 1-like 4) was previously detected to be involved in plant response to a variety of stresses. TaPYL4 overexpression could enhance wheat (Triticum aestivum) drought resistance. In order to further investigate TaPYL4's role in regulating development of other major agronomic traits in wheat, genes of TaPYL4-2A, TaPYL4-2B, and TaPYL4-2D were cloned from wheat, respectively. Polymorphism analysis on TaPYL4 sequences revealed that encoding regions of the three genes were highly conserved, without any SNP (single nucleotide polymorphism) presence. However, nine SNPs and four SNPs were identified in the promoter regions of TaPYL4-2A and TaPYL4-2B, respectively. Functional molecular markers were developed based on these polymorphisms, which were then used to scan a natural population of 323 common wheat accessions for correlation analysis between genotype and the target phenotypic traits. Both TaPYL4-2A and TaPYL4-2B markers were significantly correlated with plant growth-related traits under multiple environments (well-watered, drought and heat stress treatments). The additive effects of TaPYL4-2A and TaPYL4-2B were verified by the combinational haplotype (Hap-AB1∼Hap-AB4) effects determined from field data. Cis-acting elements were analyzed in the promoters of TaPYL4-2A and TaPYL4-2B, showing that a TGA-element bound by ARFs (auxin response factors) existed only in Hap-2A-1 of TaPYL4-2A. Gene expression assays indicated that TaPYL4-2A was constitutively expressed in various tissues, with higher expression in Hap-2A-1 genotypes than in Hap-2A-2 materials. Notably, TaARF4 could act as TaPYL4-2A transcription activator in Hap-2A-1 materials, but not in Hap-2A-2 genotypes. Analysis of geographic distribution and temporal frequency of haplotypes indicated that Hap-AB1 was positively selected in wheat breeding in China. Therefore, TaPYL4-2A and TaPYL4-2B could be a valuable target gene in wheat genetic improvement to develop the ideal plant architecture.
Collapse
Affiliation(s)
- Yinghong Xue
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xi Yang
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Chenyang Hao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Runzhi Li
- College of Agronomy, Shanxi Agricultural University, Jinzhong, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
15
|
Liu R, Hou J, Li H, Xu P, Zhang Z, Zhang X. Association of TaD14-4D, a Gene Involved in Strigolactone Signaling, with Yield Contributing Traits in Wheat. Int J Mol Sci 2021; 22:ijms22073748. [PMID: 33916852 PMCID: PMC8038469 DOI: 10.3390/ijms22073748] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/01/2021] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
Tillering is a crucial agronomic trait of wheat; it determines yield and plant architecture. Strigolactones (SLs) have been reported to inhibit plant branching. D14, a receptor of SLs, has been described to affect tillering in rice, yet it has seldomly been studied in wheat. In this study, three TaD14 homoeologous genes, TaD14-4A, TaD14-4B, and TaD14-4D, were identified. TaD14-4A, TaD14-4B, and TaD14-4D were constitutively expressed, and TaD14-4D had a higher expression level in most tissues. TaD14 proteins were localized in both cytoplasm and nucleus. An SNP and a 22 bp insertion/deletion (Indel) at the exon regions of TaD14-4D were detected, forming three haplotypes, namely 4D-HapI, 4D-HapII, and 4D-HapIII. Due to the frameshift mutation in the coding region of 4D-HapII, the interaction of 4D-HapII with TaMAX2 and TaD53 was blocked, which led to the blocking of SL signal transduction. Based on the two variation sites, two molecular markers, namely dCAPS-250 and Indel-747, were developed. Association analysis suggested that haplotypes of TaD14-4D were associated with effective tillering number (ETN) and thousand kernel weight (TKW) simultaneously in four environments. The favorable haplotype 4D-HapIII underwent positive selection in global wheat breeding. This study provides insights into understanding the function of natural variations of TaD14-4D and develops two useful molecular markers for wheat breeding.
Collapse
Affiliation(s)
- Ruifang Liu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China; (R.L.); (P.X.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.H.); (H.L.)
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.H.); (H.L.)
| | - Huifang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.H.); (H.L.)
| | - Ping Xu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China; (R.L.); (P.X.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050022, China; (R.L.); (P.X.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (Z.Z.); (X.Z.)
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.H.); (H.L.)
- Correspondence: (Z.Z.); (X.Z.)
| |
Collapse
|
16
|
Yang Y, Tian H, Wang R, Wang L, Yi H, Liu Y, Xu L, Fan Y, Zhao J, Wang F. Variety Discrimination Power: An Appraisal Index for Loci Combination Screening Applied to Plant Variety Discrimination. FRONTIERS IN PLANT SCIENCE 2021; 12:566796. [PMID: 33815430 PMCID: PMC8014032 DOI: 10.3389/fpls.2021.566796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Molecular marker technology is used widely in plant variety discrimination, molecular breeding, and other fields. To lower the cost of testing and improve the efficiency of data analysis, molecular marker screening is very important. Screening usually involves two phases: the first to control loci quality and the second to reduce loci quantity. To reduce loci quantity, an appraisal index that is very sensitive to a specific scenario is necessary to select loci combinations. In this study, we focused on loci combination screening for plant variety discrimination. A loci combination appraisal index, variety discrimination power (VDP), is proposed, and three statistical methods, probability-based VDP (P-VDP), comparison-based VDP (C-VDP), and ratio-based VDP (R-VDP), are described and compared. The results using the simulated data showed that VDP was sensitive to statistical populations with convergence toward the same variety, and the total probability of discrimination power (TDP) method was effective only for partial populations. R-VDP was more sensitive to statistical populations with convergence toward various varieties than P-VDP and C-VDP, which both had the same sensitivity; TDP was not sensitive at all. With the real data, R-VDP values for sorghum, wheat, maize and rice data begin to show downward tendency when the number of loci is 20, 7, 100, 100 respectively, while in the case of P-VDP and C-VDP (which have the same results), the number is 6, 4, 9, 19 respectively and in the case of TDP, the number is 6, 4, 4, 11 respectively. For the variety threshold setting, R-VDP values of loci combinations with different numbers of loci responded evenly to different thresholds. C-VDP values responded unevenly to different thresholds, and the extent of the response increased as the number of loci decreased. All the methods gave underestimations when data were missing, with systematic errors for TDP, C-VDP, and R-VDP going from smallest to biggest. We concluded that VDP was a better loci combination appraisal index than TDP for plant variety discrimination and the three VDP methods have different applications. We developed the software called VDPtools, which can calculate the values of TDP, P-VDP, C-VDP, and R-VDP. VDPtools is publicly available at https://github.com/caurwx1/VDPtools.git.
Collapse
|
17
|
Liu Y, Chen Y, Yang Y, Zhang Q, Fu B, Cai J, Guo W, Shi L, Wu J, Chen Y. A thorough screening based on QTLs controlling zinc and copper accumulation in the grain of different wheat genotypes. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:15043-15054. [PMID: 33230790 DOI: 10.1007/s11356-020-11690-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 11/16/2020] [Indexed: 06/11/2023]
Abstract
Excess trace metals may cause damage to human health due to the consumption of food grain grown in contaminated soils. This study was designed to understand the genetic mechanisms of copper (Cu) and zinc (Zn) accumulation in wheat grain under stressed environments. The differences of Cu/Zn contents in the grain among 246 wheat varieties were analyzed, and the wheat varieties with low or high accumulation of Cu and Zn in the safe range were also screened out. The accumulation of Cu and Zn in grains of "Chushanbao" was lowest, which could be used as a novel germplasm for wheat breeding under heavy metal stress. We found that Cu contents of wheat grain were significantly and positively correlated with Zn. The quantitative trait loci (QTLs) for grain Cu content (GCuC) and grain Zn content (GZnC) were detected by genome-wide association study (GWAS). Twenty-three loci affecting GCuC were identified on chromosomes 1A, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 4A, 4B 4D, 5A, 6D, 7A, and 7B, explaining 2.6-5.8% of the phenotypic variation. Sixteen loci associated with the GZnC on 11 different chromosomes 1B, 2B, 2D, 3A, 3D, 4A, 4B, 5A, 5D, 6B, and 7D were detected, which could explain 2.7~6.6% of phenotypic variance. We also determined five associated loci on chromosomes 2B, 2D, 3A, 4B, and 5A were in pleiotropic regions affecting both GCuC and GZnC. This study would help in better understanding the molecular basis of Cu/Zn accumulation in wheat grain, and the associated markers may be useful for marker-assisted selection (MAS) breeding program.
Collapse
Affiliation(s)
- Ying Liu
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | | | - Yang Yang
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Qiaofeng Zhang
- Provincial Key Laboratory of Agrobiology, The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Bisheng Fu
- Provincial Key Laboratory of Agrobiology, The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Jin Cai
- Provincial Key Laboratory of Agrobiology, The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Wei Guo
- Provincial Key Laboratory of Agrobiology, The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Liang Shi
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China.
| | - Jizhong Wu
- Provincial Key Laboratory of Agrobiology, The Jiangsu Provincial Infrastructure for Conservation and Utilization of Agricultural Germplasm, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China.
| | - Yahua Chen
- College of Life Sciences, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource, National Joint Local Engineering Research Center for Rural Land Resources Use and Consolidation, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| |
Collapse
|
18
|
Wu J, Yu R, Wang H, Zhou C, Huang S, Jiao H, Yu S, Nie X, Wang Q, Liu S, Weining S, Singh RP, Bhavani S, Kang Z, Han D, Zeng Q. A large-scale genomic association analysis identifies the candidate causal genes conferring stripe rust resistance under multiple field environments. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:177-191. [PMID: 32677132 PMCID: PMC7769225 DOI: 10.1111/pbi.13452] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 05/02/2023]
Abstract
The incorporation of resistance genes into wheat commercial varieties is the ideal strategy to combat stripe or yellow rust (YR). In a search for novel resistance genes, we performed a large-scale genomic association analysis with high-density 660K single nucleotide polymorphism (SNP) arrays to determine the genetic components of YR resistance in 411 spring wheat lines. Following quality control, 371 972 SNPs were screened, covering over 50% of the high-confidence annotated gene space. Nineteen stable genomic regions harbouring 292 significant SNPs were associated with adult-plant YR resistance across nine environments. Of these, 14 SNPs were localized in the proximity of known loci widely used in breeding. Obvious candidate SNP variants were identified in certain confidence intervals, such as the cloned gene Yr18 and the major locus on chromosome 2BL, despite a large extent of linkage disequilibrium. The number of causal SNP variants was refined using an independent validation panel and consideration of the estimated functional importance of each nucleotide polymorphism. Interestingly, four natural polymorphisms causing amino acid changes in the gene TraesCS2B01G513100 that encodes a serine/threonine protein kinase (STPK) were significantly involved in YR responses. Gene expression and mutation analysis confirmed that STPK played an important role in YR resistance. PCR markers were developed to identify the favourable TraesCS2B01G513100 haplotype for marker-assisted breeding. These results demonstrate that high-resolution SNP-based GWAS enables the rapid identification of putative resistance genes and can be used to improve the efficiency of marker-assisted selection in wheat disease resistance breeding.
Collapse
Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Haiying Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasNorthwest A&F UniversityYanglingShaanxiChina
| | - Cai'e Zhou
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Hanxuan Jiao
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Shengjie Liu
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Song Weining
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT)TexcocoEstado de MexicoMexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center (CIMMYT)TexcocoEstado de MexicoMexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of AgronomyNorthwest A&F UniversityYanglingShaanxiChina
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant ProtectionNorthwest A&F UniversityYanglingShaanxiChina
| |
Collapse
|
19
|
Tsonev S, Christov NK, Mihova G, Dimitrova A, Todorovska EG. Genetic diversity and population structure of bread wheat varieties grown in Bulgaria based on microsatellite and phenotypic analyses. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1996274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Stefan Tsonev
- Department of Functional Genetics, AgroBioInstitute, Agricultural Academy, Sofia, Bulgaria
| | | | - Gallina Mihova
- Department of Cereal and Legumes Breeding, Dobrudzha Agricultural Institute, Agricultural Academy, General Toshevo, Bulgaria
| | - Anna Dimitrova
- Department of Regulation of Gene Expression, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | |
Collapse
|
20
|
Li Y, Zhang Y, Li C, Chen X, Yang L, Zhang J, Wang J, Li L, Reynolds MP, Jing R, Mao X, Wang C. Transcription Factor TaWRKY51 Is a Positive Regulator in Root Architecture and Grain Yield Contributing Traits. FRONTIERS IN PLANT SCIENCE 2021; 12:734614. [PMID: 34745169 PMCID: PMC8567066 DOI: 10.3389/fpls.2021.734614] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 05/17/2023]
Abstract
Wheat is one of the staple food crops. The utilization of elite genetic resources to develop resource-efficient wheat varieties is an effective approach to deal with the challenges of climate change and population growth. WRKY transcription factors (TFs) are multifaceted regulators of plant growth and development and response to environmental stress. The previous studies have shown that TaWRKY51 positively regulates the development of lateral roots, while its roles in agronomic trait development are not clear, and there is no functional marker for molecular breeding. To bridge the gap, we cloned the three members of TaWRKY51 and found they were highly expressed in the roots and flag leaves at the flowering stage and were induced by the multiple abiotic stresses and phytohormones. The highest expression level was observed in TaWRKY51-2D, followed by TaWRKY51-2A and -2B. The two haplotypes/alleles for each member were identified in the natural populations, and functional markers were developed accordingly. The association assays revealed that Hap-2A-I was an elite haplotype for the large spike, Hap-2B-II and allele-G were favorable haplotypes/alleles for long root. However, only Hap-2A-I was selected for wheat breeding in China. The results of transgenic experiments showed that the rice lines overexpressing TaWRKY51 had large panicle, high thousand-grain-weight, and more crown and lateral roots, which further confirmed the results of association analysis. In short, TaWRKY51 is a positive regulator of the root architecture and grain yield (GY) contributing traits. The elite gene resources and functional markers may be utilized in the marker-assisted selection for high-yield breeding in wheat.
Collapse
Affiliation(s)
- Yuying Li
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanfei Zhang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lili Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jie Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jingyi Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Long Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Ruilian Jing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xinguo Mao
| | - Chenyang Wang
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
- Chenyang Wang
| |
Collapse
|
21
|
Khadka K, Torkamaneh D, Kaviani M, Belzile F, Raizada MN, Navabi A. Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm. BMC PLANT BIOLOGY 2020; 20:530. [PMID: 33225886 PMCID: PMC7682013 DOI: 10.1186/s12870-020-02722-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 10/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Appropriate information about genetic diversity and population structure of germplasm improves the efficiency of plant breeding. The low productivity of Nepali bread wheat (Triticum aestivum L.) is a major concern particularly since Nepal is ranked the 4th most vulnerable nation globally to climate change. The genetic diversity and population structure of Nepali spring wheat have not been reported. This study aims to improve the exploitation of more diverse and under-utilized genetic resources to contribute to current and future breeding efforts for global food security. RESULTS We used genotyping-by-sequencing (GBS) to characterize a panel of 318 spring wheat accessions from Nepal including 166 landraces, 115 CIMMYT advanced lines, and 34 Nepali released varieties. We identified 95 K high-quality SNPs. The greatest genetic diversity was observed among the landraces, followed by CIMMYT lines, and released varieties. Though we expected only 3 groupings corresponding to these 3 seed origins, the population structure revealed two large, distinct subpopulations along with two smaller and scattered subpopulations in between, with significant admixture. This result was confirmed by principal component analysis (PCA) and UPGMA distance-based clustering. The pattern of LD decay differed between subpopulations, ranging from 60 to 150 Kb. We discuss the possibility that germplasm explorations during the 1970s-1990s may have mistakenly collected exotic germplasm instead of local landraces and/or collected materials that had already cross-hybridized since exotic germplasm was introduced starting in the 1950s. CONCLUSION We suggest that only a subset of wheat "landraces" in Nepal are authentic which this study has identified. Targeting these authentic landraces may accelerate local breeding programs to improve the food security of this climate-vulnerable nation. Overall, this study provides a novel understanding of the genetic diversity of wheat in Nepal and this may contribute to global wheat breeding initiatives.
Collapse
Affiliation(s)
- Kamal Khadka
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Mina Kaviani
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Francois Belzile
- Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| |
Collapse
|
22
|
Zheng X, Liu C, Qiao L, Zhao J, Han R, Wang X, Ge C, Zhang W, Zhang S, Qiao L, Zheng J, Hao C. The MYB transcription factor TaPHR3-A1 is involved in phosphate signaling and governs yield-related traits in bread wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5808-5822. [PMID: 32725154 DOI: 10.1093/jxb/eraa355] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 07/23/2020] [Indexed: 06/11/2023]
Abstract
Improved inorganic phosphate (Pi) use efficiency in crops will be important for sustainable agriculture. Exploring molecular mechanisms that regulate Pi uptake could provide useful information for breeding wheat with improved Pi use efficiency. Here, a TaPHR3-A1 (Gene ID: TraesCS7A02G415800) ortholog of rice OsPHR3 that functions in transcriptional regulation of Pi signaling was cloned from wheat chromosome 7A. Ectopic expression of TaPHR3-A1 in Arabidopsis and rice produced enhanced vegetative growth and more seeds. Overexpression in transgenic rice led to increased biomass, grain number, and primary panicle branching by 61.23, 42.12, and 36.34% compared with the wild type. Transgenic wheat lines with down-regulation of TaPHR3-A1 exhibited retarded growth and root hair development at the seedling stage, and showed yield-related effects at the adult stage when grown in both low- and sufficient Pi conditions, indicating that TaPHR3-A1 positively regulated tolerance to low Pi. Introgression lines further confirmed the effect of TaPHR3-A1 in improving grain number. The Chinese wheat mini core collection and a recombinant inbred line analysis demonstrated that the favorable allele TaPHR3-A1-A associated with higher grain number was positively selected in breeding. A TaPHR3-A1-derived cleaved amplified polymorphic sequence marker effectively identified haplotype TaPHR3-A1-A. Our results suggested that TaPHR3-A1 was a functional regulatory factor for Pi uptake and provided useful information for marker-assisted selection for high yield in wheat.
Collapse
Affiliation(s)
- Xingwei Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Cheng Liu
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Ling Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jiajia Zhao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Ran Han
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Xiaolu Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Laboratory for Wheat & Maize, Jinan, China
| | - Chuan Ge
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Wenyun Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Shuwei Zhang
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Linyi Qiao
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Jun Zheng
- Institute of Wheat Research, Shanxi Agricultural University, Linfen, China
| | - Chenyang Hao
- The National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
23
|
Hou J, Liu Y, Hao C, Li T, Liu H, Zhang X. Starch Metabolism in Wheat: Gene Variation and Association Analysis Reveal Additive Effects on Kernel Weight. FRONTIERS IN PLANT SCIENCE 2020; 11:562008. [PMID: 33123177 PMCID: PMC7573188 DOI: 10.3389/fpls.2020.562008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
Kernel weight is a key determinant of yield in wheat (Triticum aestivum L.). Starch consists of amylose and amylopectin and is the major constituent of mature grain. Therefore, starch metabolism in the endosperm during grain filling can influence kernel weight. In this study, we sequenced 87 genes involved in starch metabolism from 300 wheat accessions and detected 8,141 polymorphic sites. We also characterized yield-related traits across different years in these accessions. Although the starch contents fluctuated, thousand kernel weight (TKW) showed little variation. Polymorphisms in six genes were significantly associated with TKW. These genes were located on chromosomes 2A, 2B, 4A, and 7A; none were associated with starch content or amylose content. Variations of 15 genes on chromosomes 1A and 7A formed haplotype blocks in 26 accessions. Notably, accessions with higher TKWs had more of the favorable haplotypes. We thus conclude that these haplotypes contribute additive effects to TKW.
Collapse
Affiliation(s)
- Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yunchuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| |
Collapse
|
24
|
Fu L, Wu J, Yang S, Jin Y, Liu J, Yang M, Rasheed A, Zhang Y, Xia X, Jing R, He Z, Xiao Y. Genome-wide association analysis of stem water-soluble carbohydrate content in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2897-2914. [PMID: 32594265 DOI: 10.1007/s00122-020-03640-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/19/2020] [Indexed: 05/14/2023]
Abstract
GWAS identified 36 potentially new loci for wheat stem water-soluble carbohydrate (WSC) contents and 13 pleiotropic loci affecting WSC and thousand-kernel weight. Five KASP markers were developed and validated. Water-soluble carbohydrates (WSC) reserved in stems contribute significantly to grain yield (GY) in wheat. However, knowledge of the genetic architecture underlying stem WSC content (SWSCC) is limited. In the present study, 166 diverse wheat accessions from the Yellow and Huai Valleys Winter Wheat Zone of China and five other countries were grown in four well-watered environments. SWSCC at 10 days post-anthesis (10DPA), 20DPA and 30DPA, referred as WSC10, WSC20 and WSC30, respectively, and thousand-kernel weight (TKW) were assessed. Correlation analysis showed that TKW was significantly and positively correlated with WSC10 and WSC20. Genome-wide association study was performed on SWSCC and TKW with 373,106 markers from the wheat 660 K and 90 K SNP arrays. Totally, 62 stable loci were detected for SWSCC, with 36, 24 and 19 loci for WSC10, WSC20 and WSC30, respectively; among these, 36 are potentially new, 16 affected SWSCC at two or three time-points, and 13 showed pleiotropic effects on both SWSCC and TKW. Linear regression showed clear cumulative effects of favorable alleles for increasing SWSCC and TKW. Genetic gain analyses indicated that pyramiding favorable alleles of SWSCC had simultaneously improved TKW. Kompetitive allele-specific PCR markers for five pleiotropic loci associated with both SWSCC and TKW were developed and validated. This study provided a genome-wide landscape of the genetic architecture of SWSCC, gave a perspective for understanding the relationship between WSC and GY and explored the theoretical basis for co-improvement of WSC and GY. It also provided valuable loci and markers for future breeding.
Collapse
Affiliation(s)
- Luping Fu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jingchun Wu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shurong Yang
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730000, Gansu, China
| | - Yirong Jin
- Dezhou Institute of Agricultural Sciences, Dezhou, 253000, Shandong, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences (CAAS), Shenzhen, 518000, China
| | - Mengjiao Yang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Ruilian Jing
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
- International Maize and Wheat Improvement Center (CIMMYT) China Office, Beijing, 100081, China.
| | - Yonggui Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| |
Collapse
|
25
|
Yang X, Tan B, Liu H, Zhu W, Xu L, Wang Y, Fan X, Sha L, Zhang H, Zeng J, Wu D, Jiang Y, Hu X, Chen G, Zhou Y, Kang H. Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing. Front Genet 2020; 11:580782. [PMID: 33101397 PMCID: PMC7545058 DOI: 10.3389/fgene.2020.580782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Obtaining information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N. In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content was in the range of 0.1 to 0.4, with a mean of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was slightly higher as indicated by the observed heterozygosity (H o) = 0.23, and unbiased diversity index (uh) = 0.34. The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.
Collapse
Affiliation(s)
- Xiu Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Binwen Tan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haijiao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lili Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xigui Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| |
Collapse
|
26
|
Wang J, Wang R, Mao X, Zhang J, Liu Y, Xie Q, Yang X, Chang X, Li C, Zhang X, Jing R. RING finger ubiquitin E3 ligase gene TaSDIR1-4A contributes to determination of grain size in common wheat. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5377-5388. [PMID: 32479613 PMCID: PMC7501821 DOI: 10.1093/jxb/eraa271] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/26/2020] [Indexed: 05/16/2023]
Abstract
Salt and drought-induced RING finger1 (SDIR1) is a RING-type E3 ubiquitin ligase that plays a key role in ABA-mediated responses to salinity and drought stress via the ubiquitination pathway in some plant species. However, its function in wheat (Triticum aestivum) is unknown. Here, we isolated a SDIR1 member in wheat, TaSDIR1-4A, and characterized its E3 ubiquitin ligase activity. DNA polymorphism assays showed the presence of two nucleotide variation sites in the promoter region of TaSDIR1-4A, leading to the detection of the haplotypes Hap-4A-1 and Hap-4A-2 in wheat populations. Association analysis showed that TaSDIR1-4A haplotypes were associated with 1000-grain weight (TGW) across a variety of different environments, including well-watered and heat-stress conditions. Genotypes with Hap-4A-2 had higher TGW than those with Hap-4A-1. Phenotypes in both gene-silenced wheat and transgenic Arabidopsis showed that TaSDIR1-4A was a negative regulator of grain size. Gene expression assays indicated that TaSDIR1-4A was most highly expressed in flag leaves, and expression was higher in Hap-4A-1 accessions than in Hap-4A-2 accessions. The difference might be attributable to the fact that TaERF3 (ethylene response factor) can act as a transcriptional repressor of TaSDIR1-4A in Hap-4A-2 but not in Hap-4A-1. Examination of modern wheat varieties shows that the favorable haplotype has been positively selected in breeding programs in China. The functional marker for TaSDIR1-4A developed in this study should be helpful for future wheat breeding.
Collapse
Affiliation(s)
- Jingyi Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruitong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jialing Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanna Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qi Xie
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoyuan Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiaoping Chang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chaonan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xueyong Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
27
|
Al-Ashkar I, Alotaibi M, Refay Y, Ghazy A, Zakri A, Al-Doss A. Selection criteria for high-yielding and early-flowering bread wheat hybrids under heat stress. PLoS One 2020; 15:e0236351. [PMID: 32785293 PMCID: PMC7423122 DOI: 10.1371/journal.pone.0236351] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/04/2020] [Indexed: 01/09/2023] Open
Abstract
Hybrid performance during wheat breeding can be improved by analyzing genetic distance (GD) among wheat genotypes and determining its correlation with heterosis. This study evaluated the GD between 16 wheat genotypes by using 60 simple sequence repeat (SSR) markers to classify them according to their relationships and select those with greater genetic diversity, evaluate the correlation of the SSR marker distance with heterotic performance and specific combining ability (SCA) for heat stress tolerance, and identify traits that most influence grain yield (GY). Eight parental genotypes with greater genetic diversity and their 28 F1 hybrids generated using diallel crossing were evaluated for 12 measured traits in two seasons. The GD varied from 0.235 to 0.911 across the 16 genotypes. Cluster analysis based on the GD estimated using SSRs classified the genotypes into three major groups and six sub-groups, almost consistent with the results of principal coordinate analysis. The combined data indicated that five hybrids showed 20% greater yield than mid-parent or better-parent. Two hybrids (P2 × P4) and (P2 × P5), which showed the highest performance of days to heading (DH), grain filling duration (GFD), and GY, and had large genetic diversity among themselves (0.883 and 0.911, respectively), were deemed as promising heat-tolerant hybrids. They showed the best mid-parent heterosis and better-parent heterosis (BPH) for DH (-11.57 and -7.65%; -13.39 and -8.36%, respectively), GFD (12.74 and 12.17%; 12.09 and 10.59%, respectively), and GY (36.04 and 20.04%; 44.06 and 37.73%, respectively). Correlation between GD and each of BPH and SCA effects based on SSR markers was significantly positive for GFD, hundred kernel weight, number of kernels per spike, harvest index, GY, and grain filling rate and was significantly negative for DH. These correlations indicate that the performance of wheat hybrids with high GY and earliness could be predicted by determining the GD of the parents by using SSR markers. Multivariate analysis (stepwise regression and path coefficient) suggested that GFD, hundred kernel weight, days to maturity, and number of kernels per spike had the highest influence on GY.
Collapse
Affiliation(s)
- Ibrahim Al-Ashkar
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
- Agronomy Department, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
- * E-mail:
| | - Majed Alotaibi
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Yahya Refay
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Abdelhalim Ghazy
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Adel Zakri
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah Al-Doss
- Plant Production, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| |
Collapse
|
28
|
Yang F, Liu J, Guo Y, He Z, Rasheed A, Wu L, Cao S, Nan H, Xia X. Genome-Wide Association Mapping of Adult-Plant Resistance to Stripe Rust in Common Wheat ( Triticum aestivum). PLANT DISEASE 2020; 104:2174-2180. [PMID: 32452749 DOI: 10.1094/pdis-10-19-2116-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is a globally devastating disease of common wheat (Triticum aestivum L.), resulting in substantial economic losses. To identify effective resistance genes, a genome-wide association study was conducted on 120 common wheat lines from different wheat-growing regions of China using the wheat 90K iSelect SNP array. Seventeen loci were identified, explaining 9.5 to 21.8% of the phenotypic variation. Most of these genes were detected in the A (seven) and B (seven) genomes, with only three in the D genome. Among them, 11 loci were colocated with known resistance genes or quantitative trait loci reported previously, whereas the other six are likely new resistance loci. Annotation of flanking sequences of significantly associated SNPs indicated the presence of three important candidate genes, including E3 ubiquitin-protein ligase, F-box repeat protein, and disease resistance RPP13-like protein. This study increased our knowledge in understanding the genetic architecture for stripe rust resistance and identified wheat varieties with multiple resistance alleles, which are useful for improvement of stripe rust resistance in breeding.
Collapse
Affiliation(s)
- Fangping Yang
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Jindong Liu
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518120, China
| | - Ying Guo
- Wheat Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| | - Ling Wu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, Sichuan 610066, China
| | - Shiqin Cao
- Institute of Plant Protection, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu 730070, China
| | - Hai Nan
- Tianshui Institute of Agricultural Sciences, Tianshui, Gansu 741200, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China
| |
Collapse
|
29
|
Bashir H, Bashir Z, Mahajan R, Nazir M, Mir RA, Nehvi FA, Zargar SM. Molecular characterization and insights into the origin of common bean (Phaseolus vulgaris L.) landraces of north western Himalayas. THE NUCLEUS 2020. [DOI: 10.1007/s13237-020-00323-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
|
30
|
Ma J, Lin Y, Tang S, Duan S, Wang Q, Wu F, Li C, Jiang X, Zhou K, Liu Y. A Genome-Wide Association Study of Coleoptile Length in Different Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2020; 11:677. [PMID: 32582239 PMCID: PMC7287122 DOI: 10.3389/fpls.2020.00677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/29/2020] [Indexed: 05/26/2023]
Abstract
From the perspective of wheat yield improvement, the coleoptile is vital for successful crop establishment, and long coleoptile lengths (CLs) are preferred in wheat-growing regions where deep planting is practiced. To determine the genetic basis of CL, we performed a genome-wide association study on a set of 707 Chinese wheat landraces using 18,594 single-nucleotide polymorphisms and 38,678 diversity array technology sequencing markers. We accordingly detected a total of 29 significant markers [-log10 (P) > 4.76] distributed on chromosomes 2B, 2D, 3A, 4A, 5A, 6A, 6B, 6D, and 7B. Based on linkage disequilibrium decay distance, we identified a total of 17 quantitative trait loci associated with CL, among which QCl.sicau-6B.2, located at 508.17-509.26 Mb on chromosome 6B, was recognized as a novel major locus. We subsequently developed a high-resolution melt marker for QCl.sicau-6B.2, which was validated in an F 2 : 3 population. Our findings provide important insights into the genetic mechanisms underlying coleoptile growth and could be applied to marker-assisted wheat selection.
Collapse
Affiliation(s)
- Jun Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yu Lin
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Si Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shuonan Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Qing Wang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Fangkun Wu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiaojun Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kunyu Zhou
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
| |
Collapse
|
31
|
Wu J, Wang X, Chen N, Yu R, Yu S, Wang Q, Huang S, Wang H, Singh RP, Bhavani S, Kang Z, Han D, Zeng Q. Association Analysis Identifies New Loci for Resistance to Chinese Yr26-Virulent Races of the Stripe Rust Pathogen in a Diverse Panel of Wheat Germplasm. PLANT DISEASE 2020; 104:1751-1762. [PMID: 32293995 DOI: 10.1094/pdis-12-19-2663-re] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Stripe rust caused by Puccinia striiformis f. sp. tritici (Pst) is one of the most destructive fungal diseases of wheat worldwide. The expanding Yr26-virulent Pst race (V26) group overcomes almost all currently deployed resistance genes in China and has continued to accumulate new virulence. Investigating the genetic architecture of stripe rust resistance in common wheat is an important basis for a successful utilization of resistance in breeding programs. A panel of 410 exotic wheat germplasms was used for characterizing new stripe rust resistance loci. This panel was genotyped using high-density wheat 660K single-nucleotide polymorphism (SNP) array, and phenotypic evaluation of seedlings for stripe rust resistance was performed using multiple Pst races. Thirty-five loci conferring resistance were identified through genome-wide association mapping, and explained phenotypic variances ranged from 53 to 75%. Of these, 14 were colocated in the proximity of the known loci, including cataloged Yr genes Yr9, Yr10, Yr26, Yr33, Yr47, Yr56, Yr57, Yr64, Yr67, Yr72, and Yr81 and three temporarily designated as YrCen, YrNP63, and YrRC detected in our quantitative trait locus (QTL) mapping studies. Seven of them (Yr9, Yr10, Yr24/26, Yr81, YrCEN, YrNP63, and YrRC) were confirmed by molecular detection or genetic analysis. New loci that were identified to be different from reported Yr genes need further confirmation. Nine QTL with significantly large phenotypic effect on resistance to all tested races were considered as major loci for effective resistance. The identified loci enrich our stripe rust resistance gene pool, and the linked SNPs should be useful for marker-assisted selection in breeding programs.
Collapse
Affiliation(s)
- Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Xiaoting Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Rui Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shizhou Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qilin Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Shuo Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Haiying Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Ravi P Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Sridhar Bhavani
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, Shaanxi 712100, P. R. China
| |
Collapse
|
32
|
Sun H, Zhang W, Wu Y, Gao L, Cui F, Zhao C, Guo Z, Jia J. The Circadian Clock Gene, TaPRR1, Is Associated With Yield-Related Traits in Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2020; 11:285. [PMID: 32226438 PMCID: PMC7080851 DOI: 10.3389/fpls.2020.00285] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
Timing of flowering is crucial for the transformation from vegetative to reproductive growth in the important food crop, wheat (Triticum aestivum L.). The circadian clock is a central part of photoperiod regulation, with Pseudo-Response Regulators (PRRs) representing key components of circadian networks. However, little is known about the effects of PRR family members on yield-related traits in crop plants. In this study, we identified polymorphisms and haplotypes of TaPRR1, demonstrating that natural variations in TaPRR1 are associated with significant differences in yield-related traits including heading date, plant height and thousand grain weight. TaPRR1-6A-Hapla showed an earlier heading date, advanced by 0.9 to 1.7%. TaPRR1-6B-Hapla and TaPRR1-6D-Hapla displayed reduced plant height and increased thousand grain weight of up to 13.3 to 26.4% and 6.3 to 17.3%, respectively. Subcellular localization and transcriptional activity analysis showed that TaPRR1 is a nuclear localization protein with transcriptional activity controlled by an IR domain. The expression profiles of TaPRR1 genes over a 48-h period were characterized by circadian rhythms, which had two peaks under both short- and long- day conditions. In addition, geographical distribution analysis indicated higher distribution frequencies of TaPRR1-6A-Hapla, TaPRR1-6B-Haplb, and TaPRR1-6D-Haplb in different agro-ecological production zones. Furthermore, analysis of molecular variance of the distribution frequency of TaPRR1 haplotypes suggested significant differences in haplotype distribution frequency between landraces and modern cultivars. Our study provides a basis for in-depth understanding of TaPRR1 function on yield-related traits in wheat, as well as establishing theoretical guidance for wheat molecular marker-assisted breeding.
Collapse
Affiliation(s)
- Han Sun
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Wenping Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongzhen Wu
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Lifeng Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fa Cui
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Chunhua Zhao
- College of Agriculture, Ludong University, Yantai, China
- Key Laboratory of Molecular Module-Based Breeding of High Yield and Abiotic Resistant Plants in Universities of Shandong, Ludong University, Yantai, China
| | - Zhiai Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Jizeng Jia
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| |
Collapse
|
33
|
Rio S, Mary-Huard T, Moreau L, Bauland C, Palaffre C, Madur D, Combes V, Charcosset A. Disentangling group specific QTL allele effects from genetic background epistasis using admixed individuals in GWAS: An application to maize flowering. PLoS Genet 2020; 16:e1008241. [PMID: 32130208 PMCID: PMC7075643 DOI: 10.1371/journal.pgen.1008241] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 03/16/2020] [Accepted: 01/29/2020] [Indexed: 12/21/2022] Open
Abstract
When handling a structured population in association mapping, group-specific allele effects may be observed at quantitative trait loci (QTLs) for several reasons: (i) a different linkage disequilibrium (LD) between SNPs and QTLs across groups, (ii) group-specific genetic mutations in QTL regions, and/or (iii) epistatic interactions between QTLs and other loci that have differentiated allele frequencies between groups. We present here a new genome-wide association (GWAS) approach to identify QTLs exhibiting such group-specific allele effects. We developed genetic materials including admixed progeny from different genetic groups with known genome-wide ancestries (local admixture). A dedicated statistical methodology was developed to analyze pure and admixed individuals jointly, allowing one to disentangle the factors causing the heterogeneity of allele effects across groups. This approach was applied to maize by developing an inbred "Flint-Dent" panel including admixed individuals that was evaluated for flowering time. Several associations were detected revealing a wide range of configurations of allele effects, both at known flowering QTLs (Vgt1, Vgt2 and Vgt3) and new loci. We found several QTLs whose effect depended on the group ancestry of alleles while others interacted with the genetic background. Our GWAS approach provides useful information on the stability of QTL effects across genetic groups and can be applied to a wide range of species.
Collapse
Affiliation(s)
- Simon Rio
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
- MIA, INRAE, AgroParisTech, Université Paris-Saclay, 75005, Paris, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Carine Palaffre
- UE 0394 SMH, INRAE, 2297 Route de l’INRA, 40390, Saint-Martin-de-Hinx, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190, Gif-sur-Yvette, France
| |
Collapse
|
34
|
Pariyar SR, Erginbas-Orakci G, Dadshani S, Chijioke OB, Léon J, Dababat AA, Grundler FMW. Dissecting the Genetic Complexity of Fusarium Crown Rot Resistance in Wheat. Sci Rep 2020; 10:3200. [PMID: 32081866 PMCID: PMC7035263 DOI: 10.1038/s41598-020-60190-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/28/2020] [Indexed: 11/09/2022] Open
Abstract
Fusarium crown rot (FCR) is one of the most important diseases of wheat (Triticum aestivum L.). FCR is mainly caused by the fungal pathogens Fusarium culmorum and F. pseudograminearum. In order to identify new sources of resistance to FCR and to dissect the complexity of FCR resistance, a panel of 161 wheat accessions was phenotyped under growth room (GR) and greenhouse conditions (GH). Analysis of variance showed significant differences in crown rot development among wheat accessions and high heritability of genotype-environment interactions for GR (0.96) and GH (0.91). Mixed linear model analysis revealed seven novel quantitative trait loci (QTLs) linked to F. culmorum on chromosomes 2AL, 3AS, 4BS, 5BS, 5DS, 5DL and 6DS for GR and eight QTLs on chromosomes on 3AS, 3BS, 3DL, 4BS (2), 5BS, 6BS and 6BL for GH. Total phenotypic variances (R²) explained by the QTLs linked to GR and GH were 48% and 59%, respectively. In addition, five favorable epistasis interactions among the QTLs were detected for both GR and GH with and without main effects. Epistatic interaction contributed additional variation up to 21% under GR and 7% under GH indicating strong effects of environment on the expression of QTLs. Our results revealed FCR resistance responses in wheat to be complex and controlled by multiple QTLs.
Collapse
Affiliation(s)
- Shree R Pariyar
- Forschungszentrum Jülich GmbH, Institut für Bio- und Geowissenschaften (IBG)-2, Pflanzenwissenschaften, D-52425, Jülich, Germany.,Institute of Crop Science and Resource Conservation (INRES), Molecular Phytomedicine, Karlrobert- Kreiten Strasse 13, D-53115, Bonn, Germany
| | - Gul Erginbas-Orakci
- International Maize and Wheat Improvement Centre (CIMMYT), P.K. 39 06511, Emek, Ankara, Turkey
| | - Said Dadshani
- Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, Katzenburgweg 5, D-53115, Bonn, Germany
| | - Oyiga Benedict Chijioke
- Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, Katzenburgweg 5, D-53115, Bonn, Germany
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES), Plant Breeding, Katzenburgweg 5, D-53115, Bonn, Germany
| | - Abdelfattah A Dababat
- International Maize and Wheat Improvement Centre (CIMMYT), P.K. 39 06511, Emek, Ankara, Turkey
| | - Florian M W Grundler
- Institute of Crop Science and Resource Conservation (INRES), Molecular Phytomedicine, Karlrobert- Kreiten Strasse 13, D-53115, Bonn, Germany.
| |
Collapse
|
35
|
Gahlaut V, Jaiswal V, Singh S, Balyan HS, Gupta PK. Multi-Locus Genome Wide Association Mapping for Yield and Its Contributing Traits in Hexaploid Wheat under Different Water Regimes. Sci Rep 2019; 9:19486. [PMID: 31862891 PMCID: PMC6925107 DOI: 10.1038/s41598-019-55520-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/29/2019] [Indexed: 11/20/2022] Open
Abstract
Multi-locus genome wide association study was undertaken using a set of 320 diverse spring wheat accessions, which were each genotyped for 9,626 SNPs. The association panel was grown in replicated trials in four environments [two each in irrigated (IR) and rainfed (RF) environments], and phenotypic data were recorded for five traits including days to heading, days to maturity, plant height, thousand grain weight and grain yield. Forty-six significant marker-trait associations (MTAs) were identified for five traits. These included 20 MTAs in IR and 19 MTAs in RF environments; seven additional MTAs were common to both the environments. Five of these MTAs were co-localized with previously known QTL/MTAs and the remaining MTAs were novel and add to the existing knowledge. Three desirable haplotypes for agronomic traits, one for improvement in RF environment and two for improvement in IR environment were identified. Eighteen (18) promising candidate genes (CGs) involved in seven different biological activities were also identified. The expression profiles of four (Trehalose-6-Phosphate, APETALA2/Ethylene-responsive factor, DNA-binding One Zinc Finger and Gibberellin-dioxygenases) of the 18 genes showed that they were induced by drought stress in the wheat seedlings. The MTAs, haplotypes and CG-based markers may be used in marker-assisted breeding for drought tolerance in wheat.
Collapse
Affiliation(s)
- Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, India
| | - Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | | | - H S Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India.
| |
Collapse
|
36
|
Mathew I, Shimelis H, Shayanowako AIT, Laing M, Chaplot V. Genome-wide association study of drought tolerance and biomass allocation in wheat. PLoS One 2019; 14:e0225383. [PMID: 31800595 PMCID: PMC6892492 DOI: 10.1371/journal.pone.0225383] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/04/2019] [Indexed: 11/18/2022] Open
Abstract
Genome wide association studies (GWAS) are important in discerning the genetic architecture of complex traits such as biomass allocation for improving drought tolerance and carbon sequestration potential of wheat. The objectives of this study were to deduce the population structure and marker-trait association for biomass traits in wheat under drought-stressed and non-stressed conditions. A 100-wheat (Triticum aestivum L.) genotype panel was phenotyped for days to heading (DTH), days to maturity (DTM), shoot biomass (SB), root biomass (RB), root to shoot ratio (RS) and grain yield (GY). The panel was sequenced using 15,600 single nucleotide polymorphism (SNPs) markers and subjected to genetic analysis using the compressed mixed linear model (CMLM) at false discovery rate (FDR < 0.05). Population structure analysis revealed six sub-clusters with high membership ancestry coefficient of ≤0.65 to their assigned sub-clusters. A total of 75 significant marker-trait associations (MTAs) were identified with a linkage disequilibrium threshold of 0.38 at 5cM. Thirty-seven of the MTAs were detected under drought-stressed condition and 48% were on the B genome, where most quantitative trait loci (QTLs) for RB, SB and GY were previously identified. There were seven pleiotropic markers for RB and SB that may facilitate simultaneous selection. Thirty-seven putative candidate genes were mined by gene annotation on the IWGSC RefSeq 1.1. The significant MTAs observed in this study will be useful in devising strategies for marker-assisted breeding for simultaneous improvement of drought tolerance and to enhance C sequestration capacity of wheat.
Collapse
Affiliation(s)
- Isack Mathew
- African Centre for Crop Improvement, University of KwaZulu-Natal, School of Agricultural, Earth and Environmental Sciences, Pietermaritzburg, South Africa
- * E-mail:
| | - Hussein Shimelis
- African Centre for Crop Improvement, University of KwaZulu-Natal, School of Agricultural, Earth and Environmental Sciences, Pietermaritzburg, South Africa
| | - Admire Isaac Tichafa Shayanowako
- African Centre for Crop Improvement, University of KwaZulu-Natal, School of Agricultural, Earth and Environmental Sciences, Pietermaritzburg, South Africa
| | - Mark Laing
- African Centre for Crop Improvement, University of KwaZulu-Natal, School of Agricultural, Earth and Environmental Sciences, Pietermaritzburg, South Africa
| | - Vincent Chaplot
- University of KwaZulu-Natal, School of Agricultural, Earth and Environmental Sciences, Pietermaritzburg, South Africa
- Sorbonne Universities, UPMC, IRD, CNRS, MNHN, Laboratoire d’Océanographie et du Climat: Expérimentations et approches numériques (LOCEAN), IPSL, Paris, France
| |
Collapse
|
37
|
Malik PL, Janss L, Nielsen LK, Borum F, Jørgensen H, Eriksen B, Schjoerring JK, Rasmussen SK. Breeding for dual-purpose wheat varieties using marker-trait associations for biomass yield and quality traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:3375-3398. [PMID: 31555887 DOI: 10.1007/s00122-019-03431-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
This study demonstrates that an active breeding nursery with rotation can be used to identify marker-trait associations for biomass yield and quality parameters that are important for biorefinery purposes. Wheat straw is a valuable feedstock for bioethanol production, but due to the recalcitrant nature of lignocellulose, its efficient use in biorefineries is limited by its low digestibility and difficult conversion of structural carbohydrates into free sugars. A genome-wide association study (GWAS) was conducted to search for significant SNP markers that could be used in a breeding programme to improve the value of wheat straw in a biorefinery setting. As part of a 3-year breeding programme (2013-2016), 190 winter wheat lines were phenotyped for traits that affect the yield and quality of the harvested biomass. These traits included straw yield, plant height, lodging at three growth stages and Septoria tritici blotch (STB) susceptibility. Release of glucose, xylose and arabinose was determined after hydrothermal pretreatment and enzymatic hydrolysis of the straw. The lines were genotyped using 15 K SNP markers and 5552 SNP markers could be used after filtering. Heritability for all traits ranged from 0.02 to 0.74. GWASs were conducted using CMLM, SUPER and FarmCPU algorithms, to analyse which algorithm could detect the highest number of marker-trait associations (MTAs). Comparable tendencies were obtained from CMLM and FarmCPU, but FarmCPU produced the most significant results. MTAs were obtained for lodging, harvest index, plant height, STB, glucose, xylose and arabinose at a significance level of p < 9.01 × 10-6. MTAs in chromosome 6A were observed for glucose, xylose and arabinose, and could be of importance for increasing sugar release for bioethanol production.
Collapse
Affiliation(s)
- Pernille L Malik
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Luc Janss
- Department of Molecular Biology and Genetics, Aarhus University, Blichers Alle 20, 8830, Tjele, Denmark
| | - Linda K Nielsen
- Sejet Plant Breeding, Nørremarksvej 67, 8700, Horsens, Denmark
| | - Finn Borum
- Sejet Plant Breeding, Nørremarksvej 67, 8700, Horsens, Denmark
| | - Henning Jørgensen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Birger Eriksen
- Sejet Plant Breeding, Nørremarksvej 67, 8700, Horsens, Denmark
| | - Jan K Schjoerring
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark
| | - Søren K Rasmussen
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg, Denmark.
| |
Collapse
|
38
|
Liu J, Rasheed A, He Z, Imtiaz M, Arif A, Mahmood T, Ghafoor A, Siddiqui SU, Ilyas MK, Wen W, Gao F, Xie C, Xia X. Genome-wide variation patterns between landraces and cultivars uncover divergent selection during modern wheat breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2509-2523. [PMID: 31139853 DOI: 10.1007/s00122-019-03367-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 05/17/2019] [Indexed: 05/21/2023]
Abstract
Genetic diversity, population structure, LD decay, and selective sweeps in 687 wheat accessions were analyzed, providing relevant guidelines to facilitate the use of the germplasm in wheat breeding. Common wheat (Triticum aestivum L.) is one of the most widely grown crops in the world. Landraces were subjected to strong human-mediated selection in developing high-yielding, good quality, and widely adapted cultivars. To investigate the genome-wide patterns of allelic variation, population structure and patterns of selective sweeps during modern wheat breeding, we tested 687 wheat accessions, including landraces (148) and cultivars (539) mainly from China and Pakistan in a wheat 90 K single nucleotide polymorphism array. Population structure analysis revealed that cultivars and landraces from China and Pakistan comprised three relatively independent genetic clusters. Cultivars displayed lower nucleotide diversity and a wider average LD decay across whole genome, indicating allelic erosion and a diversity bottleneck due to the modern breeding. Analysis of genetic differentiation between landraces and cultivars from China and Pakistan identified allelic variants subjected to selection during modern breeding. In total, 477 unique genome regions showed signatures of selection, where 109 were identified in both China and Pakistan germplasm. The majority of genomic regions were located in the B genome (225), followed by the A genome (175), and only 77 regions were located in the D genome. EigenGWAS was further used to identify key selection loci in modern wheat cultivars from China and Pakistan by comparing with global winter wheat and spring wheat diversity panels, respectively. A few known functional genes or loci found within these genome regions corresponded to known phenotypes for disease resistance, vernalization, quality, adaptability and yield-related traits. This study uncovered molecular footprints of modern wheat breeding and explained the genetic basis of polygenic adaptation in wheat. The results will be useful for understanding targets of modern wheat breeding, and in devising future breeding strategies to target beneficial alleles currently not pursued.
Collapse
Affiliation(s)
- Jindong Liu
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Awais Rasheed
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
- Quaid-i-Azam University, Islamabad, Pakistan
| | - Zhonghu He
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Muhammad Imtiaz
- International Maize and Wheat Improvement Center (CIMMYT) Pakistan Office, c/o National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Anjuman Arif
- National Institute of Agriculture and Biology (NIAB), Faisalabad, Pakistan
| | | | - Abdul Ghafoor
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Sadar Uddin Siddiqui
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Muhammad Kashif Ilyas
- Bio-resources Conservation Institute (BCI), National Agriculture Research Center (NARC), Islamabad, Pakistan
| | - Weie Wen
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Fengmei Gao
- Crop Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, Heilongjiang, China
| | - Chaojie Xie
- Department of Plant Genetics and Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193, China
| | - Xianchun Xia
- Institute of Crop Science, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| |
Collapse
|
39
|
Rufo R, Alvaro F, Royo C, Soriano JM. From landraces to improved cultivars: Assessment of genetic diversity and population structure of Mediterranean wheat using SNP markers. PLoS One 2019; 14:e0219867. [PMID: 31306459 PMCID: PMC6629082 DOI: 10.1371/journal.pone.0219867] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 07/02/2019] [Indexed: 11/18/2022] Open
Abstract
Assessment of genetic diversity and population structure in crops is essential for breeding and germplasm conservation. A collection of 354 bread wheat genotypes, including Mediterranean landraces and modern cultivars representative of the ones most widely grown in the Mediterranean Basin, were characterized with 11196 single nucleotide polymorphism (SNP) markers. Total genetic diversity (HT) and polymorphic information content (PIC) were 0.36 and 0.30 respectively for both landraces and modern cultivars. Linkage disequilibrium for the modern cultivars was higher than for the landraces (0.18 and 0.12, respectively). Analysis of the genetic structure showed a clear geographical pattern for the landraces, which were clustered into three subpopulations (SPs) representing the western, northern and eastern Mediterranean, whereas the modern cultivars were structured according to the breeding programmes that developed them: CIMMYT/ICARDA, France/Italy, and Balkan/eastern European countries. The modern cultivars showed higher genetic differentiation (GST) and lower gene flow (0.1673 and 2.49, respectively) than the landraces (0.1198 and 3.67, respectively), indicating a better distinction between subpopulations. The maximum gene flow was observed between landraces from the northern Mediterranean SPs and the modern cultivars released mainly by French and Italian breeding programmes.
Collapse
Affiliation(s)
- Rubén Rufo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Fanny Alvaro
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Conxita Royo
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
- * E-mail:
| |
Collapse
|
40
|
Wang Y, Hou J, Liu H, Li T, Wang K, Hao C, Liu H, Zhang X. TaBT1, affecting starch synthesis and thousand kernel weight, underwent strong selection during wheat improvement. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1497-1511. [PMID: 30753656 PMCID: PMC6411380 DOI: 10.1093/jxb/erz032] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 01/16/2019] [Indexed: 05/19/2023]
Abstract
BRITTLE1 (BT1), responsible for unidirectional transmembrane transport of ADP-glucose, plays a pivotal role in starch synthesis of cereal grain. In this study, we isolated three TaBT1 homoeologous genes located on chromosomes 6A, 6B, and 6D in common wheat. TaBT1 was mainly expressed in developing grains, and knockdown of TaBT1 in common wheat produced a decrease in grain size, thousand kernel weight (TKW), and grain total starch content. High diversity was detected at the TaBT1-6B locus, with 24 polymorphic sites forming three haplotypes (Hap1, Hap2, and Hap3). Association analysis revealed that Hap1 and Hap2 were preferred haplotypes in modern breeding, for their significant correlations with higher TKW. Furthermore, β-glucuronidase (GUS) staining and enzyme activity assays in developing grains of transgenic rice with exogenous promoters indicated that the promoters of Hap1 and Hap2 showed stronger driving activity than that of Hap3. Evolutionary analysis revealed that BT1 underwent strong selection during wheat polyploidization. In addition, the frequency distribution of TaBT1-6B haplotypes revealed that Hap1 and Hap2 were preferred in global modern wheat cultivars. Our findings suggest that TaBT1 has an important effect on starch synthesis and TKW, and provide two valuable molecular markers for marker assisted selection (MAS) in wheat high-yield breeding.
Collapse
Affiliation(s)
- Yamei Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hong Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Crop Genomics and Bioinformatics Center and National Key Lab of Crop Genetics and Germplasm Enhancement, College of Agricultural Sciences, Nanjing Agricultural University, Weigang, Nanjing, Jiangsu, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Ke Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- Correspondence:
| |
Collapse
|
41
|
Liu H, Li T, Wang Y, Zheng J, Li H, Hao C, Zhang X. TaZIM-A1 negatively regulates flowering time in common wheat (Triticum aestivum L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2019; 61:359-376. [PMID: 30226297 DOI: 10.1111/jipb.12720] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/11/2018] [Indexed: 05/13/2023]
Abstract
Flowering time is a critical determinant of regional adaptation for crops and has strong effects on crop yields. Here, we report that TaZIM-A1, an atypical GATA-like transcription factor, is a negative regulator of flowering in wheat. TaZIM-A1 possessed weak transcriptional repression activity, with its CCT domain functioning as the major inhibitory region. TaZIM-A1 expression exhibited a typical circadian oscillation pattern under various light regimes. Overexpression of TaZIM-A1 caused a delay in flowering time and a decrease in thousand-kernel weight (TKW) in wheat under long-day conditions. Moreover, TaZIM-A1 directly bound to the promoters of TaCO-1 and TaFT-1 and downregulated their expression. Sequence analysis of a collection of common wheat cultivars identified three and two haplotypes for TaZIM-A1 and TaZIM-B1, respectively. Association analysis revealed that TaZIM-A1-HapI/-HapIII and TaZIM-B1-HapI have undergone strong positive selection during modern wheat breeding, likely due to their association with earlier heading and higher TKW. Diagnostic markers were developed for these haplotypes that can be used for wheat cultivar improvement, via marker-assisted breeding.
Collapse
Affiliation(s)
- Hong Liu
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yamei Wang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jun Zheng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huifang Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueyong Zhang
- College of Agricultural Sciences, Nanjing Agricultural University, Nanjing, 210095, China
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| |
Collapse
|
42
|
Watson-Haigh NS, Suchecki R, Kalashyan E, Garcia M, Baumann U. DAWN: a resource for yielding insights into the diversity among wheat genomes. BMC Genomics 2018; 19:941. [PMID: 30558550 PMCID: PMC6296097 DOI: 10.1186/s12864-018-5228-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 11/06/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysing these data sets. RESULTS DAWN (Diversity Among Wheat geNomes) integrates data from the T. aestivum Chinese Spring (CS) IWGSC RefSeq v1.0 genome with public WGS and exome data from 17 and 62 accessions respectively, enabling researchers and breeders alike to investigate genotypic differences between wheat accessions at the level of whole chromosomes down to individual genes. CONCLUSIONS Using DAWN we show that it is possible to visualise small and large chromosomal deletions, identify haplotypes at a glance and spot the consequences of selective breeding. DAWN allows us to detect the break points of alien introgression segments brought into an accession when transferring desired genes. Furthermore, we can find possible explanations for reduced recombination in parts of a chromosome, we can predict regions with linkage drag, and also look at diversity in centromeric regions.
Collapse
Affiliation(s)
- Nathan S. Watson-Haigh
- School of Agriculture, Food and Wine, University of Adelaide, PMB 1, Glen Osmond, 5064 SA Australia
- Bioinformatics Hub, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005 Australia
| | - Radosław Suchecki
- School of Agriculture, Food and Wine, University of Adelaide, PMB 1, Glen Osmond, 5064 SA Australia
- CSIRO Agriculture and Food, Glen Osmond, Locked Bag 2, Adelaide, SA 5064 Australia
| | - Elena Kalashyan
- School of Agriculture, Food and Wine, University of Adelaide, PMB 1, Glen Osmond, 5064 SA Australia
| | - Melissa Garcia
- School of Agriculture, Food and Wine, University of Adelaide, PMB 1, Glen Osmond, 5064 SA Australia
| | - Ute Baumann
- School of Agriculture, Food and Wine, University of Adelaide, PMB 1, Glen Osmond, 5064 SA Australia
| |
Collapse
|
43
|
Maulana F, Ayalew H, Anderson JD, Kumssa TT, Huang W, Ma XF. Genome-Wide Association Mapping of Seedling Heat Tolerance in Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:1272. [PMID: 30233617 PMCID: PMC6131858 DOI: 10.3389/fpls.2018.01272] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/14/2018] [Indexed: 05/21/2023]
Abstract
Heat stress during the seedling stage of early-planted winter wheat (Triticum aestivum L.) is one of the most abiotic stresses of the crop restricting forage and grain production in the Southern Plains of the United States. To map quantitative trait loci (QTLs) and identify single-nucleotide polymorphism (SNP) markers associated with seedling heat tolerance, a genome-wide association mapping study (GWAS) was conducted using 200 diverse representative lines of the hard red winter wheat association mapping panel, which was established by the Triticeae Coordinated Agricultural Project (TCAP) and genotyped with the wheat iSelect 90K SNP array. The plants were initially planted under optimal temperature conditions in two growth chambers. At the three-leaf stage, one chamber was set to 40/35°C day/night as heat stress treatment, while the other chamber was kept at optimal temperature (25/20°C day/night) as control for 14 days. Data were collected on leaf chlorophyll content, shoot length, number of leaves per seedling, and seedling recovery after removal of heat stress treatment. Phenotypic variability for seedling heat tolerance among wheat lines was observed in this study. Using the mixed linear model (MLM), we detected multiple significant QTLs for seedling heat tolerance on different chromosomes. Some of the QTLs were detected on chromosomes that were previously reported to harbor QTLs for heat tolerance during the flowering stage of wheat. These results suggest that some heat tolerance QTLs are effective from the seedling to reproductive stages in wheat. However, new QTLs that have never been reported at the reproductive stage were found responding to seedling heat stress in the present study. Candidate gene analysis revealed high sequence similarities of some significant loci with candidate genes involved in plant stress responses including heat, drought, and salt stress. This study provides valuable information about the genetic basis of seedling heat tolerance in wheat. To the best of our knowledge, this is the first GWAS to map QTLs associated with seedling heat tolerance targeting early planting of dual-purpose winter wheat. The SNP markers identified in this study will be used for marker-assisted selection (MAS) of seedling heat tolerance during dual-purpose wheat breeding.
Collapse
Affiliation(s)
- Frank Maulana
- Noble Research Institute, Ardmore, OK, United States
| | | | | | | | - Wangqi Huang
- Noble Research Institute, Ardmore, OK, United States
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Xue-Feng Ma
- Noble Research Institute, Ardmore, OK, United States
| |
Collapse
|
44
|
Fayaz F, Aghaee Sarbarzeh M, Talebi R, Azadi A. Genetic Diversity and Molecular Characterization of Iranian Durum Wheat Landraces (Triticum turgidum durum (Desf.) Husn.) Using DArT Markers. Biochem Genet 2018; 57:98-116. [PMID: 30051349 DOI: 10.1007/s10528-018-9877-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 07/14/2018] [Indexed: 01/07/2023]
Abstract
Durum wheat is grown mainly in rain-fed regions of Iran and the Mediterranean district under stressful conditions. Different environmental conditions and agricultural practices among ancient communities have led to the development of locally adapted genotypes known as landraces. Landraces are a valued source of genetic variety and show definite adaptation to local environmental conditions according to their home of origin. This study aimed to explore linkage disequilibrium (LD) analysis and the population structure and genetic diversity of Iranian durum wheat landraces. In this study, population structure and genome-wide LD were investigated in 129 durum landrace accessions using 1500 DArT markers. Both structure and discriminant analysis of principal components obviously subdivided the sample collection into seven distinct groups centered on key ancestors and regions of origin of the germplasm. Genetic diversity among the populations was primarily within population (68 vs. 32%). Mean LD values across the entire population sample decayed below r2 of 0.11 after 1 cM. LD decay of genomes A and B of Iranian durum wheat landrace is approximately 2-3 cM (r2 = 0.11) and approximately 0.5 cM (r2 = 0.12), respectively. Altogether, low LD decay, a high number of subpopulations, and the high existence of genetic diversity among and within populations were characteristics of the Iranian durum landrace collection. Hence, the existing genetic diversity within the population can be associated with the very long evolutionary history of plants in Iran. The populations we studied are hence presented as a valuable resource that can be used in basic and applied research in durum wheat breeding.
Collapse
Affiliation(s)
- Farzad Fayaz
- Department of Agronomy & Plant Breeding, College of Agriculture, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran.
| | - Mostafa Aghaee Sarbarzeh
- Seed and Plant Improvement Institute, Agriculture Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Reza Talebi
- Department of Agronomy & Plant Breeding, College of Agriculture, Islamic Azad University, Sanandaj Branch, Sanandaj, Iran
| | - Amin Azadi
- Department of Plant Breeding, Yadegar-e-Imam Khomeini (RAH), Islamic Azad University, Shahre Rey Branch, Tehran, Iran
| |
Collapse
|
45
|
Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B, Sehgal SK. Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018; 9:926. [PMID: 30034404 PMCID: PMC6043670 DOI: 10.3389/fpls.2018.00926] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 06/11/2018] [Indexed: 05/06/2023]
Abstract
Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
Collapse
Affiliation(s)
| | | | | | | | | | - Sunish K. Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| |
Collapse
|
46
|
Zhou YJ, Yang Q, Zhong XJ, Tang HP, Deng M, Ma J, Qi PF, Wang JR, Chen GY, Liu YX, Lu ZX, Li W, Lan XJ, Wei YM, Zheng YL, Jiang QT. Alternative splicing results in a lack of starch synthase IIa-D in Chinese wheat landrace. Genome 2018; 61:201-208. [PMID: 29401409 DOI: 10.1139/gen-2017-0246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We evaluated the SGP-1 protein composition of 368 Chinese wheat landraces using SDS-PAGE. The SGP-D1 null type was identified in three accessions (Xiaoqingmang, Pushanbamai, and P119). An 18-bp deletion and 9-bp variation were found at the junction region of the 7th intron and 8th exon, leading to deletion of the intron-exon junction recognition site AG when aligned the 8261-bp DNA sequence of TaSSIIa-D in Pushanbamai with that of Chinese Spring. Four cDNA types with mis-spliced isoforms were subsequently detected through amplification of TaSSIIa-D cDNAs. Among these, nine type II cDNAs with a 16-bp deletion in the 8th exon were detected, indicating that the major transcriptional pattern of TaSSIIa in Pushanbamai is type II. In the type IV cDNA, a 97-bp sequence remains undeleted in the end of the 5th exon. The amylose content in Pushanbamai was significantly higher than that in all control lines under field conditions, which suggested that deletion of SGP-D1 has an efficient impact on amylose content. As the TaSSIIa gene plays an important role in regulating the content of amylose, it is anticipated that these natural variants of TaSSIIa-D will provide useful resources for quality improvement in wheat.
Collapse
Affiliation(s)
- Yan-Jie Zhou
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qiang Yang
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiao-Juan Zhong
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Hua-Ping Tang
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Mei Deng
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Jian Ma
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Peng-Fei Qi
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Ji-Rui Wang
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Guo-Yue Chen
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Ya-Xi Liu
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Zhen-Xiang Lu
- b Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada
| | - Wei Li
- c College of Agronomy, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Xiu-Jin Lan
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Yu-Ming Wei
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - You-Liang Zheng
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Qian-Tao Jiang
- a Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| |
Collapse
|
47
|
Ayana GT, Ali S, Sidhu JS, Gonzalez Hernandez JL, Turnipseed B, Sehgal SK. Genome-Wide Association Study for Spot Blotch Resistance in Hard Winter Wheat. FRONTIERS IN PLANT SCIENCE 2018. [PMID: 30034404 DOI: 10.3389/fpls00926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Spot blotch (SB) caused by Cochliobolus sativus (anamorph: Bipolaris sorokiniana) is an economically important disease of wheat worldwide. Under a severe epidemic condition, the disease can cause yield losses up to 70%. Previous approaches like bi-parental mapping for identifying SB resistant genes/QTLs exploited only a limited portion of the available genetic diversity with a lower capacity to detect polygenic traits, and had a lower marker density. In this study, we performed genome-wide association study (GWAS) for SB resistance in hard winter wheat association mapping panel (HWWAMP) of 294 genotypes. The HWWAMP was evaluated for response to B. sorokiniana (isolate SD40), and a range of reactions was observed with 10 resistant, 38 moderately resistant, 120 moderately resistant- moderately susceptible, 111 moderately susceptible, and 15 susceptible genotypes. GWAS using 15,590 high-quality SNPs and 294 genotypes we identified six QTLs (p = <0.001) on chromosomes 2D, 3A, 4A, 4B, 5A, and 7B that collectively explained 30% of the total variation for SB resistance. Highly associated SNPs were identified for all six QTLs, QSb.sdsu-2D.1 (SNP: Kukri_c31121_1460, R2 = 4%), QSb.sdsu-3A.1 (SNP: Excalibur_c46082_440, R2 = 4%), QSb.sdsu-4A.1 (SNP: IWA8475, R2 = 5.5%), QSb.sdsu-4B.1 (SNP: Excalibur_rep_c79414_306, R2 = 4%), QSb.sdsu-5A.1 (SNP: Kukri_rep_c104877_2166, R2 = 6%), and QSb.sdsu-7B.1 (SNP: TA005844-0160, R2 = 6%). Our study not only validates three (2D, 5A, and 7B) genomic regions identified in previous studies but also provides highly associated SNP markers for marker assisted selection. In addition, we identified three novel QTLs (QSb.sdsu-3A.1, QSb.sdsu-4A.1, and QSb.sdsu-4B.1) for SB resistance in wheat. Gene annotation analysis of the candidate regions identified nine NBS-LRR and 38 other plant defense-related protein families across multiple QTLs, and these could be used for fine mapping and further characterization of SB resistance in wheat. Comparative analysis with barley indicated the SB resistance locus on wheat chromosomes 2D, 3A, 5A, and 7B identified in our study are syntenic to the previously identified SB resistance locus on chromosomes 2H, 3H, 5H, and 7H in barley. The 10 highly resistant genotypes and SNP markers identified in our study could be very useful resources for breeding of SB resistance in wheat.
Collapse
Affiliation(s)
- Girma T Ayana
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Shaukat Ali
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jagdeep S Sidhu
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Jose L Gonzalez Hernandez
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Brent Turnipseed
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Sunish K Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| |
Collapse
|
48
|
Norman A, Taylor J, Tanaka E, Telfer P, Edwards J, Martinant JP, Kuchel H. Increased genomic prediction accuracy in wheat breeding using a large Australian panel. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:2543-2555. [PMID: 28887586 PMCID: PMC5668360 DOI: 10.1007/s00122-017-2975-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/19/2017] [Indexed: 05/28/2023]
Abstract
KEY MESSAGE Genomic prediction accuracy within a large panel was found to be substantially higher than that previously observed in smaller populations, and also higher than QTL-based prediction. In recent years, genomic selection for wheat breeding has been widely studied, but this has typically been restricted to population sizes under 1000 individuals. To assess its efficacy in germplasm representative of commercial breeding programmes, we used a panel of 10,375 Australian wheat breeding lines to investigate the accuracy of genomic prediction for grain yield, physical grain quality and other physiological traits. To achieve this, the complete panel was phenotyped in a dedicated field trial and genotyped using a custom AxiomTM Affymetrix SNP array. A high-quality consensus map was also constructed, allowing the linkage disequilibrium present in the germplasm to be investigated. Using the complete SNP array, genomic prediction accuracies were found to be substantially higher than those previously observed in smaller populations and also more accurate compared to prediction approaches using a finite number of selected quantitative trait loci. Multi-trait genetic correlations were also assessed at an additive and residual genetic level, identifying a negative genetic correlation between grain yield and protein as well as a positive genetic correlation between grain size and test weight.
Collapse
Affiliation(s)
- Adam Norman
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, Australia.
- Australian Grain Technologies Pty Ltd, Perkins Building, Roseworthy Campus, Roseworthy, SA, Australia.
| | - Julian Taylor
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
| | - Emi Tanaka
- National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, University of Wollongong, Wollongong, NSW, Australia
| | - Paul Telfer
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
- Australian Grain Technologies Pty Ltd, Perkins Building, Roseworthy Campus, Roseworthy, SA, Australia
| | - James Edwards
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
- Australian Grain Technologies Pty Ltd, Perkins Building, Roseworthy Campus, Roseworthy, SA, Australia
| | | | - Haydn Kuchel
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA, Australia
- Australian Grain Technologies Pty Ltd, Perkins Building, Roseworthy Campus, Roseworthy, SA, Australia
| |
Collapse
|
49
|
Hou J, Li T, Wang Y, Hao C, Liu H, Zhang X. ADP-glucose pyrophosphorylase genes, associated with kernel weight, underwent selection during wheat domestication and breeding. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1533-1543. [PMID: 28371241 PMCID: PMC5698054 DOI: 10.1111/pbi.12735] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/23/2017] [Accepted: 03/26/2017] [Indexed: 05/04/2023]
Abstract
ADP-glucose pyrophosphorylase, comprising two small subunits and two large subunits, is considered a key enzyme in the endosperm starch synthesis pathway in wheat (Triticum aestivum L.). Two genes, TaAGP-S1-7A and TaAGP-L-1B, were investigated in this study. Haplotypes of these genes were associated with thousand kernel weight (TKW) in different populations. Mean TKWs of favoured haplotypes were significantly higher than those of nonfavoured ones. Two molecular markers developed to distinguish these haplotypes could be used in molecular breeding. Frequencies of favoured haplotypes were dramatically increased in cultivars released in China after the 1940s. These favoured haplotypes were also positively selected in six major wheat production regions globally. Selection of AGP-S1 and AGP-L-1B in wheat mainly occurred during and after hexaploidization. Strong additive effects of the favoured haplotypes of with other genes for starch synthesis were also detected in different populations.
Collapse
Affiliation(s)
- Jian Hou
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Tian Li
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Yamei Wang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Chenyang Hao
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Hongxia Liu
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xueyong Zhang
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| |
Collapse
|
50
|
Liu J, He Z, Rasheed A, Wen W, Yan J, Zhang P, Wan Y, Zhang Y, Xie C, Xia X. Genome-wide association mapping of black point reaction in common wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2017; 17:220. [PMID: 29169344 PMCID: PMC5701291 DOI: 10.1186/s12870-017-1167-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 11/10/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Black point is a serious threat to wheat production and can be managed by host resistance. Marker-assisted selection (MAS) has the potential to accelerate genetic improvement of black point resistance in wheat breeding. We performed a genome-wide association study (GWAS) using the high-density wheat 90 K and 660 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of black point resistance and identify associated molecular markers. RESULTS Black point reactions were evaluated in 166 elite wheat cultivars in five environments. Twenty-five unique loci were identified on chromosomes 2A, 2B, 3A, 3B (2), 3D, 4B (2), 5A (3), 5B (3), 6A, 6B, 6D, 7A (5), 7B and 7D (2), respectively, explaining phenotypic variation ranging from 7.9 to 18.0%. The highest number of loci was detected in the A genome (11), followed by the B (10) and D (4) genomes. Among these, 13 were identified in two or more environments. Seven loci coincided with known genes or quantitative trait locus (QTL), whereas the other 18 were potentially novel loci. Linear regression showed a clear dependence of black point scores on the number of favorable alleles, suggesting that QTL pyramiding will be an effective approach to increase resistance. In silico analysis of sequences of resistance-associated SNPs identified 6 genes possibly involved in oxidase, signal transduction and stress resistance as candidate genes involved in black point reaction. CONCLUSION SNP markers significantly associated with black point resistance and accessions with a larger number of resistance alleles can be used to further enhance black point resistance in breeding. This study provides new insights into the genetic architecture of black point reaction.
Collapse
Affiliation(s)
- Jindong Liu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
- Department of Plant Genetics & Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081 China
| | - Awais Rasheed
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Weie Wen
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Jun Yan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), 38 Huanghe Street, Anyang, Henan 455000 China
| | - Pingzhi Zhang
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, Anhui 230001 China
| | - Yingxiu Wan
- Crop Research Institute, Anhui Academy of Agricultural Sciences, 40 Nongke South Street, Hefei, Anhui 230001 China
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| | - Chaojie Xie
- Department of Plant Genetics & Breeding/State Key Laboratory for Agrobiotechnology, China Agricultural University, 2 Yuanmingyuan West Road, Beijing, 100193 China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081 China
| |
Collapse
|