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Reddy SS, Saini DK, Singh GM, Sharma S, Mishra VK, Joshi AK. Genome-wide association mapping of genomic regions associated with drought stress tolerance at seedling and reproductive stages in bread wheat. FRONTIERS IN PLANT SCIENCE 2023; 14:1166439. [PMID: 37251775 PMCID: PMC10213333 DOI: 10.3389/fpls.2023.1166439] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/14/2023] [Indexed: 05/31/2023]
Abstract
Understanding the genetic architecture of drought stress tolerance in bread wheat at seedling and reproductive stages is crucial for developing drought-tolerant varieties. In the present study, 192 diverse wheat genotypes, a subset from the Wheat Associated Mapping Initiative (WAMI) panel, were evaluated at the seedling stage in a hydroponics system for chlorophyll content (CL), shoot length (SLT), shoot weight (SWT), root length (RLT), and root weight (RWT) under both drought and optimum conditions. Following that, a genome-wide association study (GWAS) was carried out using the phenotypic data recorded during the hydroponics experiment as well as data available from previously conducted multi-location field trials under optimal and drought stress conditions. The panel had previously been genotyped using the Infinium iSelect 90K SNP array with 26,814 polymorphic markers. Using single as well as multi-locus models, GWAS identified 94 significant marker-trait associations (MTAs) or SNPs associated with traits recorded at the seedling stage and 451 for traits recorded at the reproductive stage. The significant SNPs included several novel, significant, and promising MTAs for different traits. The average LD decay distance for the whole genome was approximately 0.48 Mbp, ranging from 0.07 Mbp (chromosome 6D) to 4.14 Mbp (chromosome 2A). Furthermore, several promising SNPs revealed significant differences among haplotypes for traits such as RLT, RWT, SLT, SWT, and GY under drought stress. Functional annotation and in silico expression analysis revealed important putative candidate genes underlying the identified stable genomic regions such as protein kinases, O-methyltransferases, GroES-like superfamily proteins, NAD-dependent dehydratases, etc. The findings of the present study may be useful for improving yield potential, and stability under drought stress conditions.
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Affiliation(s)
- S Srinatha Reddy
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - G Mahendra Singh
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Sandeep Sharma
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Arun Kumar Joshi
- Borlaug Institute of South Asia (BISA), NASC Complex, DPS Marg, New Delhi, India
- CIMMYT, NASC Complex, DPS Marg, New Delhi, India
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2
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Zhang Y, Miao H, Wang C, Zhang J, Zhang X, Shi X, Xie S, Li T, Deng P, Wang C, Chen C, Zhang H, Ji W. Genetic identification of the pleiotropic gene Tasg-D1/2 affecting wheat grain shape by regulating brassinolide metabolism. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 323:111392. [PMID: 35868348 DOI: 10.1016/j.plantsci.2022.111392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/08/2022] [Accepted: 07/16/2022] [Indexed: 06/15/2023]
Abstract
Improving yield potential is a major goal of wheat breeding that depends on identifying key genetic loci. In this study, two residual heterozygous line RHL351- and RHL78-derived populations were employed for genetic linkage map construction and QTL detection. Two genetic populations indicated a robust grain-size QTL between Marker6 and Marker10. It covered a 95.54-99.38 Mb physical interval and was named Qpleio.nwafu.3D, containing the candidate gene Tasg (TraesCS3D02G137200). Intriguingly, RNA-seq analysis and sequencing revealed two different allelic variants in Tasg, named Tasg-D1 (G>A) and Tasg-D2 (C>G), respectively. Although the relationship between Tasg-D1 and grain size had been demonstrated previously, here we provided the first genetic evidence that C/G allelic variation in Tasg-D2 was associated with grain shape and size through a newly developed dCAPS marker. In addition, transcriptome comparison indicated that Tasg-D1/2 might primarily contribute to significant expression differences in brassinolide (BR) metabolism-related genes rather than those related to BR responses in developing grains and spikes. Our study provided new evidence and a breeder-friendly dCAPS marker for improving grain size through the selection of Tasg, as well as a basis to understand Tasg function in the future.
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Affiliation(s)
- Yaoyuan Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Hanxiao Miao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Chao Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Junjie Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiangyu Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Xiaoxi Shi
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Songfeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
| | - Tingdong Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Pingchuan Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Changyou Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Chunhuan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China
| | - Hong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China.
| | - Wanquan Ji
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China; Shaanxi Research Station of Crop Gene Resources and Germplasm Enhancement, Ministry of Agriculture, Yangling 712100, China.
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3
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Wang C, Zhang L, Xie Y, Guo X, Zhang Y, Zhang Y, Irshad A, Li Y, Qian H, Jing D, Liu G, Wu K, Yang N, Yang G, Song Y, Guo H, Zhao H, Wang C, Liu L, Zhang G, Ma S. A superior allele of the wheat gene TaGL3.3-5B, selected in the breeding process, contributes to seed size and weight. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1879-1891. [PMID: 35377004 DOI: 10.1007/s00122-022-04081-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
A superior allele of wheat gene TaGL3.3-5B was identified and could be used in marker-assisted breeding in wheat. Identifying the main genes which mainly regulate the yield-associated traits can significantly increase the wheat production. In this study, gene TaGL3.3 was cloned from common wheat according to the sequence of OsPPKL3. A SNP in the 8th exon of TaGL3.3-5B, T/C in coding sequence (CDS), which resulted in an amino acid change (Val/Ala), was identified between the low 1000-kernel weight (TKW) wheat Chinese Spring and the high TKW wheat Xinong 817 (817). Subsequently, association analysis in the mini-core collection (MCC) and the recombinant inbred lines (RIL) revealed that the allele TaGL3.3-5B-C (from 817) was significantly correlated with higher TKW. The high frequency of TaGL3.3-5B-C in the Chinese modern wheat cultivars indicated that it was selected positively in wheat breeding programs. The overexpression of TaGL3.3-5B-C in Arabidopsis resulted in shorter pods and longer grains than those of wild-type counterparts. Additionally, TaGL3.3 expressed a tissue-specific pattern in wheat as revealed by qRT-PCR. We also found that 817 showed higher expression of TaGL3.3 than that in Chinese Spring (CS) during the seed development. These results demonstrate that TaGL3.3 plays an important role in the formation of seed size and weight. Allele TaGL3.3-5B-C is associated with larger and heavier grains that are beneficial to wheat yield improvement.
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Affiliation(s)
- Chaojie Wang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Lili Zhang
- Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, 712100, Shaanxi, People's Republic of China
- College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yongdun Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Xiaofeng Guo
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yanfang Zhang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yamin Zhang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Ahsan Irshad
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Yuting Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Huihui Qian
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Doudou Jing
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Guangyao Liu
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Kaiming Wu
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Na Yang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Guoli Yang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Yulong Song
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Huijun Guo
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China
| | - Huiyan Zhao
- College of Plant Protection, Northwest A & F University, Yangling, 712100, Shaanxi, People's Republic of China
| | - Chengshe Wang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China
| | - Luxiang Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Engineering Laboratory of Crop Molecular Breeding, National Center of Space Mutagenesis for Crop Improvement, Beijing, 100081, People's Republic of China.
| | - Gaisheng Zhang
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, 712100, Shaanxi, People's Republic of China.
| | - Shoucai Ma
- College of Agronomy, Northwest A & F University, National Yangling Agricultural Biotechnology & Breeding Center, Yangling, 712100, Shaanxi, People's Republic of China.
- Key Laboratory of Crop Heterosis of Shaanxi Province, Yangling, 712100, Shaanxi, People's Republic of China.
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Jing F, Miao Y, Zhang P, Chen T, Liu Y, Ma J, Li M, Yang D. Characterization of TaSPP-5A gene associated with sucrose content in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2022; 22:58. [PMID: 35105304 PMCID: PMC8805233 DOI: 10.1186/s12870-022-03442-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 01/18/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND Sucrose, the major product of photosynthesis and the primary sugar transported as a soluble carbohydrate via the phloem, is a critical determinant for harvest yield in wheat crops. Sucrose-phosphatase (SPP) catalyzes the final step in the sucrose biosynthesis pathway, implying its essential role in the plant. RESULT In this study, wheat SPP homologs genes were isolated from chromosomes 5A, 5B, and 5D, designated as TaSPP-5A, TaSPP-5B, and TaSPP-5D, respectively. Sequence alignment showed one 1-bp Insertion-deletion (InDel) and three single nucleotide polymorphisms (SNPs) at TaSPP-5A coding region, forming two haplotypes, TaSPP-5Aa and TaSPP-5Ab, respectively. A derived cleaved amplified polymorphism sequence (dCAPS) marker, TaSPP-5A-dCAPS, was developed to discriminate allelic variation based on the polymorphism at position 1242 (C-T). A total of 158 varieties were used to perform a TaSPP-5A marker-trait association analysis, where two haplotypes were significantly associated with sucrose content in two environments and with thousand-grain weight (TGW) and grain length (GL) in three environments. Quantitative real-time PCR further revealed that TaSPP-5Aa showed relatively higher expression than TaSPP-5Ab in wheat seedling leaves, generally associating with increased sucrose content and TGW. The expression of TaSPP-5A and sucrose content in TaSPP-5Aa haplotypes were also higher than those in TaSPP-5Ab haplotypes under both 20% PEG-6000 and 100 μM ABA treatment. Sequence alignment showed that the two TaSPP-5A haplotypes comprised 11 SNPs from -395 to -1962 bp at TaSPP-5A promoter locus, participating in the formation of several conserved sequences, may account for the high expression of TaSPP-5A in TaSPP-5Aa haplotypes. In addition, the distribution analysis of TaSPP-5A haplotypes revealed that TaSPP-5Aa was preferred in the natural wheat population, being strongly positively selected in breeding programs. CONCLUSION According to the SNPs detected in the TaSPP-5A sequence, two haplotypes, TaSPP-5Aa and TaSPP-5Ab, were identified among wheat accessions, which potential value for sucrose content selection was validated by association analysis. Our results indicate that the favorable allelic variation TaSPP-5Aa should be valuable in enhancing grain yield by improving the sucrose content. Furthermore, a functional marker, TaSPP-5A-dCAPS, can be used for marker-assisted selection to improve grain weight in wheat and provides insights into the biological function of TaSPP-5A gene.
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Affiliation(s)
- Fanli Jing
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Yongping Miao
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Peipei Zhang
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China
| | - Tao Chen
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Yuan Liu
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Jingfu Ma
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Mengfei Li
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China
| | - Delong Yang
- Gansu Provincial Key Lab of Aridland Crop Science, Lanzhou, 730070, Gansu, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, Gansu, China.
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Zhao D, Yang L, Liu D, Zeng J, Cao S, Xia X, Yan J, Song X, He Z, Zhang Y. Fine mapping and validation of a major QTL for grain weight on chromosome 5B in bread wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3731-3741. [PMID: 34324015 DOI: 10.1007/s00122-021-03925-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
A major QTL QTgw.caas-5B for thousand grain weight in wheat was fine mapped on chromosome 5B, and TraesCS5B02G044800 was predicted to be the candidate gene. Thousand grain weight (TGW), determined by grain length and width, and is an important yield component in wheat; understanding of the underlying genes and molecular mechanisms remains limited. A stable QTL QTgw.caas-5B for TGW was identified previously in a RIL population developed from a cross between Zhongmai 871 (ZM871) and a sister line Zhongmai 895 (ZM895), and the aim of this study was to perform fine mapping and validate the genetic effect of the QTL. It was delimited to an interval of approximately 2.0 Mb flanked by markers Kasp_5B29 and Kasp_5B31 (49.6-51.6 Mb) using 12 heterozygous recombinant plants obtained by selfing a residual BC1F6 line selected from the ZM871/ZM895//ZM871 population. A candidate gene was predicted following sequencing and differential expression analyses. Marker Kasp_5B_Tgw based on a SNP in TraesCS5B02G044800, the QTgw.caas-5B candidate, was developed and validated in a diversity panel of 166 cultivars. The precise mapping of QTgw.caas-5B laid a foundation for cloning of a predicted causal gene and provides a molecular marker for improving grain yield in wheat.
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Affiliation(s)
- Dehui Zhao
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Li Yang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Dan Liu
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jianqi Zeng
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Jun Yan
- Institute of Cotton Research, CAAS, 38 Huanghe Dadao, Anyang, 455000, Henan, China
| | - Xiyue Song
- College of Agronomy, Northwest A & F University, Yangling, 712100, Shaanxi, China
| | - Zhonghu He
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
- CIMMYT-China Office, C/O CAAS, Beijing, 100081, China.
| | - Yong Zhang
- Institute of Crop Sciences, National Wheat Improvement Centre, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
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Cao J, Shang Y, Xu D, Xu K, Cheng X, Pan X, Liu X, Liu M, Gao C, Yan S, Yao H, Gao W, Lu J, Zhang H, Chang C, Xia X, Xiao S, Ma C. Identification and Validation of New Stable QTLs for Grain Weight and Size by Multiple Mapping Models in Common Wheat. Front Genet 2020; 11:584859. [PMID: 33262789 PMCID: PMC7686802 DOI: 10.3389/fgene.2020.584859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 09/21/2020] [Indexed: 11/13/2022] Open
Abstract
Improvement of grain weight and size is an important objective for high-yield wheat breeding. In this study, 174 recombinant inbred lines (RILs) derived from the cross between Jing 411 and Hongmangchun 21 were used to construct a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq). Three mapping methods, including inclusive composite interval mapping (ICIM), genome-wide composite interval mapping (GCIM), and a mixed linear model performed with forward-backward stepwise (NWIM), were used to identify QTLs for thousand grain weight (TGW), grain width (GW), and grain length (GL). In total, we identified 30, 15, and 18 putative QTLs for TGW, GW, and GL that explain 1.1-33.9%, 3.1%-34.2%, and 1.7%-22.8% of the phenotypic variances, respectively. Among these, 19 (63.3%) QTLs for TGW, 10 (66.7%) for GW, and 7 (38.9%) for GL were consistent with those identified by genome-wide association analysis in 192 wheat varieties. Five new stable QTLs, including 3 for TGW (Qtgw.ahau-1B.1, Qtgw.ahau-4B.1, and Qtgw.ahau-4B.2) and 2 for GL (Qgl.ahau-2A.1 and Qgl.ahau-7A.2), were detected by the three aforementioned mapping methods across environments. Subsequently, five cleaved amplified polymorphic sequence (CAPS) markers corresponding to these QTLs were developed and validated in 180 Chinese mini-core wheat accessions. In addition, 19 potential candidate genes for Qtgw.ahau-4B.2 in a 0.31-Mb physical interval were further annotated, of which TraesCS4B02G376400 and TraesCS4B02G376800 encode a plasma membrane H+-ATPase and a serine/threonine-protein kinase, respectively. These new QTLs and CAPS markers will be useful for further marker-assisted selection and map-based cloning of target genes.
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Affiliation(s)
- Jiajia Cao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Yaoyao Shang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Dongmei Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Kangle Xu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xinran Cheng
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xu Pan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xue Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Mingli Liu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Chang Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Shengnan Yan
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Hui Yao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Wei Gao
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Jie Lu
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Haiping Zhang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Cheng Chang
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shihe Xiao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Chuanxi Ma
- KeyLaboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, College of Agronomy, Anhui Agricultural University, Hefei, China
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Guan P, Shen X, Mu Q, Wang Y, Wang X, Chen Y, Zhao Y, Chen X, Zhao A, Mao W, Guo Y, Xin M, Hu Z, Yao Y, Ni Z, Sun Q, Peng H. Dissection and validation of a QTL cluster linked to Rht-B1 locus controlling grain weight in common wheat (Triticum aestivum L.) using near-isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2639-2653. [PMID: 32488301 DOI: 10.1007/s00122-020-03622-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/22/2020] [Indexed: 05/23/2023]
Abstract
This study dissected and validated a QTL cluster associated with thousand grain weight on chromosome 4B using multiple near-isogenic lines in common wheat. Grain size and weight are crucial components of wheat yield. Previously, we identified a QTL cluster for thousand grain weight (TGW) on chromosome 4B using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population. Here, near-isogenic lines (NILs) in the ND3338 background were developed to dissect and validate the QTL cluster. Based on six independent BC3F3:4 heterogeneous inbred families, the 4B QTL cluster was divided into two linked QTL intervals (designated 4B.1 and 4B.2 QTL). For the 4B.1 QTL, the Rht-B1 gene, of which Rht-B1b allele reduces plant height (PH) by 21.18-29.34 cm (34.34-53.71%), was demonstrated to be the most likely candidate gene with pleiotropic effects on grain size and TGW. For the 4B.2 QTL, the NILJD6 consistently showed an increase in TGW of 3.51-7.68 g (8.84-22.77%) compared with NILND3338 across different field trials, along with a significant increase in PH of 2.26-6.71 cm (3.92-12.01%). Moreover, both QTL intervals had a larger effect on grain width than on grain length. Additionally, the first significant difference in 100-grain fresh weight and 100-grain dry weight between the NIL pairs of the 4B.1 QTL interval (Rht-B1) was observed at 6 days after pollination (DAP), while the differences were first visible at 30 DAP for the 4B.2 QTL interval. Collectively, our work provides a new example of QTL dissection for grain weight in wheat and lays a foundation for further map-based cloning of the major QTL that have potential applications in wheat molecular breeding for high yield.
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Affiliation(s)
- Panfeng Guan
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xueyi Shen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qing Mu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yue Zhao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiyong Chen
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Aiju Zhao
- Hebei Crop Genetic Breeding Laboratory, Institute of Cereal and Oil Crops of Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, China
| | - Weiwei Mao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yiwen Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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Cao S, Xu D, Hanif M, Xia X, He Z. Genetic architecture underpinning yield component traits in wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1811-1823. [PMID: 32062676 DOI: 10.1007/s00122-020-03562-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 02/06/2020] [Indexed: 05/19/2023]
Abstract
Genetic atlas, reliable QTL and candidate genes of yield component traits in wheat were figured out, laying concrete foundations for map-based gene cloning and dissection of regulatory mechanisms underlying yield. Mining genetic loci for yield is challenging due to the polygenic nature, large influence of environment and complex relationship among yield component traits (YCT). Many genetic loci related to wheat yield have been identified, but its genetic architecture and key genetic loci for selection are largely unknown. Wheat yield potential can be determined by three YCT, thousand kernel weight, kernel number per spike and spike number. Here, we summarized the genetic loci underpinning YCT from QTL mapping, association analysis and homology-based gene cloning. The major loci determining yield-associated agronomic traits, such as flowering time and plant height, were also included in comparative analyses with those for YCT. We integrated yield-related genetic loci onto chromosomes based on their physical locations. To identify the major stable loci for YCT, 58 QTL-rich clusters (QRC) were defined based on their distribution on chromosomes. Candidate genes in each QRC were predicted according to gene annotation of the wheat reference genome and previous information on validation of those genes in other species. Finally, a technological route was proposed to take full advantage of the resultant resources for gene cloning, molecular marker-assisted breeding and dissection of molecular regulatory mechanisms underlying wheat yield.
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Affiliation(s)
- Shuanghe Cao
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.
| | - Dengan Xu
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Mamoona Hanif
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, 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), c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China.
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9
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Gupta PK, Balyan HS, Sharma S, Kumar R. Genetics of yield, abiotic stress tolerance and biofortification in wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1569-1602. [PMID: 32253477 DOI: 10.1007/s00122-020-03583-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 03/13/2020] [Indexed: 05/18/2023]
Abstract
A review of the available literature on genetics of yield and its component traits, tolerance to abiotic stresses and biofortification should prove useful for future research in wheat in the genomics era. The work reviewed in this article mainly covers the available information on genetics of some important quantitative traits including yield and its components, tolerance to abiotic stresses (heat, drought, salinity and pre-harvest sprouting = PHS) and biofortification (Fe/Zn and phytate contents with HarvestPlus Program) in wheat. Major emphasis is laid on the recent literature on QTL interval mapping and genome-wide association studies, giving lists of known QTL and marker-trait associations. Candidate genes for different traits and the cloned and characterized genes for yield traits along with the molecular mechanism are also described. For each trait, an account of the present status of marker-assisted selection has also been included. The details of available results have largely been presented in the form of tables; some of these tables are included as supplementary files.
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Affiliation(s)
- Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India.
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
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10
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Development and identification of three functional markers associated with starch content in lotus (Nelumbo nucifera). Sci Rep 2020; 10:4242. [PMID: 32144321 PMCID: PMC7060276 DOI: 10.1038/s41598-020-60736-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 02/17/2020] [Indexed: 11/15/2022] Open
Abstract
It have been significantly demonstrated that Hexokinase (HXK), Granule-bound starch synthase (GBSS) and ADP-glucose pyrophosphorylase (AGPase) are three critical enzymes in the starch biosynthetic pathway and are related to starch (amylose, amylopectin and total starch) content in lotus. It is important to develop functional markers in marker-assisted selection of lotus breeding. So far there have been few reports about lotus functional markers. In this study, based on insertion-deletions (INDELs) and single-nucleotide polymorphisms (SNPs), we developed three functional markers, FMHXK-E1, FMGBSS-I8 and FMAGPL-I1. FMHXK-E1 was developed based on polymorphisms of two haplotypes of NnHXK. 26 lotus cultivars that the 320-bp fragment presented in NnHXK had a lower content of amylose and a higher content of amylopectin. FMGBSS-I8 was developed based on polymorphisms of two haplotypes of NnGBSS. The group containing 32 lotus cultivars with the 210-bp fragment had less amylose content and more amylopectin content. FMAGPL-I1 was developed based on polymorphisms of two haplotypes of NnAGPL (ADP-glucose pyrophosphorylase large subunit gene). The group containing 40 lotus cultivars with the 362-bp fragment had less amylopectin, total starch content and more amylose content. According to the study, FMHXK-E1, FMGBSS-I8 and FMAGPL-I1 are closely related to lotus starch content. It could be provided research basis for molecular assisted selection of lotus starch content improve breeding efficiency.
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11
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Guan P, Di N, Mu Q, Shen X, Wang Y, Wang X, Yu K, Song W, Chen Y, Xin M, Hu Z, Guo W, Yao Y, Ni Z, Sun Q, Peng H. Use of near-isogenic lines to precisely map and validate a major QTL for grain weight on chromosome 4AL in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2367-2379. [PMID: 31119311 DOI: 10.1007/s00122-019-03359-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/08/2019] [Indexed: 06/09/2023]
Abstract
This study precisely mapped and validated a major quantitative trait locus (QTL) on chromosome 4AL for thousand-grain weight in wheat using multiple near-isogenic lines. Thousand-grain weight (TGW) is an essential yield component. Following the previous identification of a major QTL for TGW within the interval of 15.7 cM (92.7-108.4 cM) on chromosome 4AL using the Nongda3338 (ND3338)/Jingdong6 (JD6) doubled haploid population, the aim of this study was to perform more precise mapping and validate the genetic effect of the QTL. Multiple near-isogenic lines (NILs) were developed using ND3338 as the recurrent parent through marker-assisted selection. Based on five independent BC3F3:4 segregating populations derived from BC3F3 plants with different heterozygous segments for the target QTL site and the results of genotyping analysis performed using the Wheat660 K SNP array, it was possible to delimit the QTL region to a physical interval of approximately 6.5 Mb (677.11-683.61 Mb, IWGSC Ref Seq v1.0). Field trials across multiple environments showed that NILsJD6 had a consistent effect on increasing the TGW by 5.16-27.48% and decreasing the grain number per spike (GNS) by 3.98-32.91% compared to the corresponding NILsND3338, which exhibited locus-specific TGW-GNS trade-offs. Moreover, by using RNA sequencing (RNA-Seq) of whole grains at 10 days after pollination stage of multiple NILs, we found that differentially expressed genes between the NIL pairs were significantly enriched for cell cycle and the replication of chromosome-related genes, hence affecting cell division and cell proliferation. Overall, our results provide a basis for map-based cloning of the major QTL and determining the mechanisms underlying TGW-GNS trade-offs in wheat, which would help to fine-tune these two components and maximize the grain yield for breeders.
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Affiliation(s)
- Panfeng Guan
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Na Di
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Qing Mu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xueyi Shen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongfa Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Xiaobo Wang
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Kuohai Yu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Wanjun Song
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yongming Chen
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhaorong Hu
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Yingyin Yao
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Huiru Peng
- State Key Laboratory for Agrobiotechnology/Key Laboratory of Crop Heterosis and Utilization, Ministry of Education/Beijing Key Laboratory of Crop Genetic Improvement/College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China.
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12
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Desiderio F, Zarei L, Licciardello S, Cheghamirza K, Farshadfar E, Virzi N, Sciacca F, Bagnaresi P, Battaglia R, Guerra D, Palumbo M, Cattivelli L, Mazzucotelli E. Genomic Regions From an Iranian Landrace Increase Kernel Size in Durum Wheat. FRONTIERS IN PLANT SCIENCE 2019; 10:448. [PMID: 31057571 PMCID: PMC6482228 DOI: 10.3389/fpls.2019.00448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/25/2019] [Indexed: 05/27/2023]
Abstract
Kernel size and shape are important parameters determining the wheat profitability, being main determinants of yield and its technological quality. In this study, a segregating population of 118 recombinant inbred lines, derived from a cross between the Iranian durum landrace accession "Iran_249" and the Iranian durum cultivar "Zardak", was used to investigate durum wheat kernel morphology factors and their relationships with kernel weight, and to map the corresponding QTLs. A high density genetic map, based on wheat 90k iSelect Infinium SNP assay, comprising 6,195 markers, was developed and used to perform the QTL analysis for kernel length and width, traits related to kernel shape and weight, and heading date, using phenotypic data from three environments. Overall, a total of 31 different QTLs and 9 QTL interactions for kernel size, and 21 different QTLs and 5 QTL interactions for kernel shape were identified. The landrace Iran_249 contributed the allele with positive effect for most of the QTLs related to kernel length and kernel weight suggesting that the landrace might have considerable potential toward enhancing the existing gene pool for grain shape and size traits and for further yield improvement in wheat. The correlation among traits and co-localization of corresponding QTLs permitted to define 11 clusters suggesting causal relationships between simplest kernel size trait, like kernel length and width, and more complex secondary trait, like kernel shape and weight related traits. Lastly, the recent release of the T. durum reference genome sequence allowed to define the physical interval of our QTL/clusters and to hypothesize novel candidate genes inspecting the gene content of the genomic regions associated to target traits.
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Affiliation(s)
- Francesca Desiderio
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Leila Zarei
- Department of Agronomy and Plant Breeding, Razi University, Kermanshah, Iran
| | - Stefania Licciardello
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | | | | | - Nino Virzi
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Fabiola Sciacca
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Paolo Bagnaresi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Raffaella Battaglia
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Davide Guerra
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Massimo Palumbo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, Acireale, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
| | - Elisabetta Mazzucotelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy
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13
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Wang J, Li R, Mao X, Jing R. Functional Analysis and Marker Development of TaCRT-D Gene in Common Wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1557. [PMID: 28955354 PMCID: PMC5601976 DOI: 10.3389/fpls.2017.01557] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2017] [Accepted: 08/25/2017] [Indexed: 05/16/2023]
Abstract
Calreticulin (CRT), an endoplasmic reticulum (ER)-localized Ca2+-binding/buffering protein, is highly conserved and extensively expressed in animal and plant cells. To understand the function of CRTs in wheat (Triticum aestivum L.), particularly their roles in stress tolerance, we cloned the full-length genomic sequence of the TaCRT-D isoform from D genome of common hexaploid wheat, and characterized its function by transgenic Arabidopsis system. TaCRT-D exhibited different expression patterns in wheat seedling under different abiotic stresses. Transgenic Arabidopsis plants overexpressing ORF of TaCRT-D displayed more tolerance to drought, cold, salt, mannitol, and other abiotic stresses at both seed germination and seedling stages, compared with the wild-type controls. Furthermore, DNA polymorphism analysis and gene mapping were employed to develop the functional markers of this gene for marker-assistant selection in wheat breeding program. One SNP, S440 (T→C) was detected at the TaCRT-D locus by genotyping a wheat recombinant inbred line (RIL) population (114 lines) developed from Opata 85 × W7984. The TaCRT-D was then fine mapped between markers Xgwm645 and Xgwm664 on chromosome 3DL, corresponding to genetic distances of 3.5 and 4.4 cM, respectively, using the RIL population and Chinese Spring nulli-tetrasomic lines. Finally, the genome-specific and allele-specific markers were developed for the TaCRT-D gene. These findings indicate that TaCRT-D function importantly in plant stress responses, providing a gene target for genetic engineering to increase plant stress tolerance and the functional markers of TaCRT-D for marker-assistant selection in wheat breeding.
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Affiliation(s)
- Jiping Wang
- College of Agronomy, Shanxi Agricultural UniversityJinzhong, China
| | - Runzhi Li
- College of Agronomy, Shanxi Agricultural UniversityJinzhong, China
| | - Xinguo Mao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Ruilian Jing
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
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14
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Hackauf B, Haffke S, Fromme FJ, Roux SR, Kusterer B, Musmann D, Kilian A, Miedaner T. QTL mapping and comparative genome analysis of agronomic traits including grain yield in winter rye. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1801-1817. [PMID: 28567664 DOI: 10.1007/s00122-017-2926-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
Genetic diversity in elite rye germplasm as well as F 2:3 testcross design enables fast QTL mapping to approach genes controlling grain yield, grain weight, tiller number and heading date in rye hybrids. Winter rye (Secale cereale L.) is a multipurpose cereal crop closely related to wheat, which offers the opportunity for a sustainable production of food and feed and which continues to emerge as a renewable energy source for the production of bioethanol and biomethane. Rye contributes to increase agricultural crop species diversity particularly in Central and Eastern Europe. In contrast to other small grain cereals, knowledge on the genetic architecture of complex inherited, agronomic important traits is yet limited for the outbreeding rye. We have performed a QTL analysis based on a F2:3 design and testcross performance of 258 experimental hybrids in multi-environmental field trials. A genetic linkage map covering 964.9 cM based on SSR, conserved-orthologous set (COS), and mixed-phase dominant DArT markers allowed to describe 22 QTL with significant effects for grain yield, heading date, tiller number, and thousand grain weight across seven environments. Using rye COS markers, orthologous segments for these traits have been identified in the rice genome, which carry cloned and functionally characterized rice genes. The initial genome scan described here together with the existing knowledge on candidate genes provides the basis for subsequent analyses of the genetic and molecular mechanisms underlying agronomic important traits in rye.
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Affiliation(s)
- Bernd Hackauf
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, 18190, Sanitz, Germany.
| | - Stefan Haffke
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
- Bundessortenamt, Osterfelddamm 80, 30627, Hannover, Germany
| | | | - Steffen R Roux
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, 18190, Sanitz, Germany
| | | | - Dörthe Musmann
- Julius Kühn-Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, Groß Lüsewitz, 18190, Sanitz, Germany
- HYBRO Saatzucht GmbH and Co. KG, 17291, Schenkenberg, Germany
| | - Andrzej Kilian
- Diversity Arrays Technology, Bruce, ACT, 2617, Australia
| | - Thomas Miedaner
- State Plant Breeding Institute, University of Hohenheim, 70593, Stuttgart, Germany
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15
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Dong Y, Zhang Y, Xiao Y, Yan J, Liu J, Wen W, Zhang Y, Jing R, Xia X, He Z. Cloning of TaSST genes associated with water soluble carbohydrate content in bread wheat stems and development of a functional marker. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1061-70. [PMID: 26883047 DOI: 10.1007/s00122-016-2683-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 01/23/2016] [Indexed: 05/21/2023]
Abstract
We cloned TaSST genes, developed a gene-specific marker for TaSST-D1, and identified three QTL in the Doumai/Shi 4185 RIL population. TaSST-D1 is within one of the three QTL. Sucrose:sucrose-1-fructosyltransferase (1-SST), a critical enzyme in the fructan biosynthetic pathway, is significantly and positively associated with water soluble carbohydrate (WSC) content in bread wheat stems. In the present study, wheat 1-SST genes (TaSST) were isolated and located on chromosomes 4A, 7A and 7D. Sequence analysis of TaSST-D1 revealed 15 single nucleotide polymorphisms (SNP) in the third exon between cultivars with higher and lower WSC content. A cleaved amplified polymorphism sequence (CAPS) marker, WSC7D, based on the polymorphism at position 1216 (C-G) was developed to discriminate the two alleles. WSC7D was located on chromosome 7DS using a recombinant inbred line (RIL) population from a Doumai/Shi 4185 cross, and a set of Chinese Spring nullisomic-tetrasomic lines. TaSST-D1 co-segregated with the CAPS marker WSC7D and was linked to SNP marker BS00108793_51 on chromosome 7DS at a genetic distance of 6.1 cM. It explained 8.8, 10.9, and 11.3% of the phenotypic variances in trials at Beijing and Shijiazhuang as well as the averaged data from those environments, respectively. Two additional QTL (QWSC.caas-4BS and QWSC.caas-7AS) besides TaSST-D1 were mapped in the RIL population. One hundred and forty-nine Chinese wheat cultivars and advanced lines tested in four environments were used to validate a highly significant (P < 0.01) association between WSC7D and WSC content in wheat stems. WSC7D can be used as a gene-specific marker for improvement of stem WSC content in wheat breeding programs.
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Affiliation(s)
- Yan Dong
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Yan Zhang
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Yonggui Xiao
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Jun Yan
- Cotton Research Institute, CAAS, Huanghedadao, Anyang, Henan, China
| | - Jindong Liu
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Weie Wen
- College of Agronomy, Xinjiang Agricultural University, 311 Nongda East Road, 830052, Urumqi, Xinjiang, China
| | - Yong Zhang
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Ruilian Jing
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
| | - Xianchun Xia
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China.
| | - Zhonghu He
- National Wheat Improvement Center, Institute of Crop Science, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, 100081, Beijing, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, 100081, Beijing, China
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Mohler V, Albrecht T, Castell A, Diethelm M, Schweizer G, Hartl L. Considering causal genes in the genetic dissection of kernel traits in common wheat. J Appl Genet 2016; 57:467-476. [PMID: 27108336 DOI: 10.1007/s13353-016-0349-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 04/06/2016] [Accepted: 04/11/2016] [Indexed: 11/25/2022]
Abstract
Genetic factors controlling thousand-kernel weight (TKW) were characterized for their association with other seed traits, including kernel width, kernel length, ratio of kernel width to kernel length (KW/KL), kernel area, and spike number per m2 (SN). For this purpose, a genetic map was established utilizing a doubled haploid population derived from a cross between German winter wheat cultivars Pamier and Format. Association studies in a diversity panel of elite cultivars supplemented genetic analysis of kernel traits. In both populations, genomic signatures of 13 candidate genes for TKW and kernel size were analyzed. Major quantitative trait loci (QTL) for TKW were identified on chromosomes 1B, 2A, 2D, and 4D, and their locations coincided with major QTL for kernel size traits, supporting the common belief that TKW is a function of other kernel traits. The QTL on chromosome 2A was associated with TKW candidate gene TaCwi-A1 and the QTL on chromosome 4D was associated with dwarfing gene Rht-D1. A minor QTL for TKW on chromosome 6B coincided with TaGW2-6B. The QTL for kernel dimensions that did not affect TKW were detected on eight chromosomes. A major QTL for KW/KL located at the distal tip of chromosome arm 5AS is being reported for the first time. TaSus1-7A and TaSAP-A1, closely linked to each other on chromosome 7A, could be related to a minor QTL for KW/KL. Genetic analysis of SN confirmed its negative correlation with TKW in this cross. In the diversity panel, TaSus1-7A was associated with TKW. Compared to the Pamier/Format bi-parental population where TaCwi-A1a was associated with higher TKW, the same allele reduced grain yield in the diversity panel, suggesting opposite effects of TaCwi-A1 on these two traits.
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Affiliation(s)
- Volker Mohler
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 8, 85354, Freising, Germany.
| | - Theresa Albrecht
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 8, 85354, Freising, Germany
| | - Adelheid Castell
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 8, 85354, Freising, Germany
| | - Manuela Diethelm
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 8, 85354, Freising, Germany
| | - Günther Schweizer
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 8, 85354, Freising, Germany
| | - Lorenz Hartl
- Institute for Crop Science and Plant Breeding, Bavarian State Research Center for Agriculture, Am Gereuth 8, 85354, Freising, Germany
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Lu J, Chang C, Zhang HP, Wang SX, Sun G, Xiao SH, Ma CX. Identification of a Novel Allele of TaCKX6a02 Associated with Grain Size, Filling Rate and Weight of Common Wheat. PLoS One 2015; 10:e0144765. [PMID: 26657796 PMCID: PMC4685998 DOI: 10.1371/journal.pone.0144765] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/23/2015] [Indexed: 11/25/2022] Open
Abstract
Cytokinin oxidase (CKX) plays a crucial role in plant growth and development by reversibly inactivating cytokinin (CTK). Twenty-four primer pairs, designed from ESTs of the TaCKX genes family of common wheat, were used to identify their allelic variations associated with grain size, weight, and filling rate in 169 recombinant inbred lines (RIL) derived from Jing 411 × Hongmangchun 21. TaCKX6a02, a member of TaCKX gene family, amplified by primer pair T31–32, showed a close association with grain traits in this RIL population. Statistical analysis indicated that allelic variation of TaCKX6a02 had significant correlation with grain size, weight, and filling rate (GFR; P < 0.001) under varied environments. The TaCKX6a02-D1a allele from Jing411 significantly increased grain size, weight and grain filling rate, compared with TaCKX6a02-D1b from Hongmangchun 21. TaCKX6a02 was located on chromosome 3DS in the interval of Xbarc1119 and Xbarc1162, with a genetic distance of 1.4 cM. The location was further confirmed using Chinese Spring nulli–tetrasomic lines. A major QTL (quantitative trait locus) tightly linked to TaCKX6a02 was detected in the RIL population, explaining 17.1~38.2% of phenotype variations for grain size, weight, GFRmax and GFRmean in different environments. In addition, significant effects of variations of TaCKX6a02 on grain weight and GFR were further validated by association analysis among 102 wheat varieties in two cropping seasons. 12.8~35.1% of phenotypic variations were estimated for these genotypes. A novel 29-bp InDel behind the stop codon was detected by DNA sequence analysis between the two alleles of TaCKX6a02-D1. The gene-specific marker, TKX3D, was designed according to the novel variation, and can be used in marker-assisted selection (MAS) for grain size, weight, and GFR in common wheat.
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Affiliation(s)
- Jie Lu
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, the Ministry of Agriculture, Hefei, 230036, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, the Ministry of Agriculture, Hefei, 230036, China
| | - Hai-Ping Zhang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, the Ministry of Agriculture, Hefei, 230036, China
| | - Sheng-Xing Wang
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, the Ministry of Agriculture, Hefei, 230036, China
| | - Genlou Sun
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, the Ministry of Agriculture, Hefei, 230036, China
- Department of Biology, Saint Mary’s University, Halifax, NS, B3H3C3, Canada
- * E-mail: (GS); (CXM)
| | - Shi-He Xiao
- Institute of Crop Sciences, National Wheat Improvement Centre/The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chuan-Xi Ma
- College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, the Ministry of Agriculture, Hefei, 230036, China
- * E-mail: (GS); (CXM)
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18
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Jaiswal V, Gahlaut V, Mathur S, Agarwal P, Khandelwal MK, Khurana JP, Tyagi AK, Balyan HS, Gupta PK. Identification of Novel SNP in Promoter Sequence of TaGW2-6A Associated with Grain Weight and Other Agronomic Traits in Wheat (Triticum aestivum L.). PLoS One 2015; 10:e0129400. [PMID: 26076351 PMCID: PMC4468092 DOI: 10.1371/journal.pone.0129400] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 05/07/2015] [Indexed: 11/18/2022] Open
Abstract
TaGW2 is an orthologue of rice gene OsGW2, which encodes E3 RING ubiquitin ligase and controls the grain size in rice. In wheat, three copies of TaGW2 have been identified and mapped on wheat homoeologous group 6 viz. TaGW2-6A, TaGW2-6B and TaGW2-6D. In the present study, using as many as 207 Indian wheat genotypes, we identified four SNPs including two novel SNPs (SNP-988 and SNP-494) in the promoter sequence of TaGW2-6A. All the four SNPs were G/A or A/G substitutions (transitions). Out of the four SNPs, SNP-494 was causal, since it was found associated with grain weight. The mean TGW (41.1 g) of genotypes with the allele SNP-494_A was significantly higher than mean TGW (38.6 g) of genotypes with the allele SNP-494_G. SNP-494 also regulates the expression of TaGW2-6A so that the wheat genotypes with SNP-494_G have higher expression and lower TGW and the genotypes with SNP-494_A have lower expression but higher TGW. Besides, SNP-494 was also found associated with grain length-width ratio, awn length, spike length, grain protein content, peduncle length and plant height. This suggested that gene TaGW2-6A not only controls grain size, but also controls other agronomic traits. In the promoter region, SNP-494 was present in 'CGCG' motif that plays an important role in Ca2+/calmodulin mediated regulation of genes. A user-friendly CAPS marker was also developed to identify the desirable allele of causal SNP (SNP-494) for use in marker-assisted selection for improvement of grain weight in wheat. Using four SNPs, five haplotypes were identified; of these, Hap_5 (G_A_G_A) was found to be a desirable haplotype having significantly higher grain weight (41.13g) relative to other four haplotypes (36.33-39.16 g).
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Affiliation(s)
- Vandana Jaiswal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Vijay Gahlaut
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Saloni Mathur
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India
| | - Priyanka Agarwal
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | | | - Jitendra Paul Khurana
- Interdisciplinary Centre for Plant Genomics, University of Delhi South Campus, New Delhi, India
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, India
| | | | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, India
- * E-mail:
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