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Tang B, Yang H, Yin Q, Miao W, Lei Y, Cui Q, Cheng J, Zhang X, Chen Y, Du J, Xie L, Tang S, Wang M, Li J, Cao M, Chen L, Xie F, Li X, Zhu F, Wang Z, Xiong C, Dai X, Zou X, Liu F. Fertility restorer gene CaRf and PepperSNP50K provide a promising breeding system for hybrid pepper. HORTICULTURE RESEARCH 2024; 11:uhae223. [PMID: 39415972 PMCID: PMC11480663 DOI: 10.1093/hr/uhae223] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 07/28/2024] [Indexed: 10/19/2024]
Abstract
Cytoplasmic male sterility (CMS) is pivotal in plant breeding and widely employed in various crop hybrids, including pepper. However, the functional validation of the restorer of fertility (Rf) gene in pepper has been lacking until now. This study identifies and characterizes CaRf, a single dominant locus crucial for restoring CMS in the pepper strong recovery inbred line Zhangshugang. The CaRf gene encodes a mitochondria-targeted pentatricopeptide repeat protein, validated through the induction of male sterility upon its silencing in hybrid F1 plants. To enhance pepper breeding efficiency, 176 important pepper breeding parent materials were resequenced, and a PepperSNP50K liquid-phase breeding chip was developed, comprising 51 172 markers. Integration of CaRf functional characterization and PepperSNP50K facilitated the development of a high-quality red pepper hybrid. These findings provide significant insights and practical strategies for advancing molecular-designed breeding in peppers.
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Affiliation(s)
- Bingqian Tang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Huiping Yang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Qinbiao Yin
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Wu Miao
- Hunan Xiangyan Seed Industry Co., Ltd, Changsha 410125, China
| | - Yuting Lei
- Higentec Co. Ltd., Changsha, Hunan, 410125, China
| | - Qingzhi Cui
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Jiawen Cheng
- Higentec Co. Ltd., Changsha, Hunan, 410125, China
| | - Xinhao Zhang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Ying Chen
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Juan Du
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Lingling Xie
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Shunxue Tang
- Higentec Co. Ltd., Changsha, Hunan, 410125, China
| | - Meiqi Wang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Jiayue Li
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Mingyue Cao
- Higentec Co. Ltd., Changsha, Hunan, 410125, China
| | - Li Chen
- Institute of Vegetable Research, Hunan Academy of Agricultural Science, Changsha 410125, China
| | - Fangling Xie
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Xiumin Li
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Fan Zhu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Zhongyi Wang
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Cheng Xiong
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Xiongze Dai
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Xuexiao Zou
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Feng Liu
- Engineering Research Center of Education, Ministry for Germplasm Innovation and Breeding New Varieties of Horticultural Crops, Key Laboratory for Vegetable Biology of Hunan Province, College of Horticulture, Hunan Agricultural University, Changsha 410128, China
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Dharsini VD, Subramanian A, Premalatha N, Boopathi NM, Djanaguiraman M, Santhanakrishnan VP. Fertile grounds: exploring male sterility in cotton and its marker development. Mol Biol Rep 2024; 51:961. [PMID: 39235637 DOI: 10.1007/s11033-024-09893-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024]
Abstract
The high cost of producing conventional hybrid cotton seeds led to more research efforts on cotton male sterility systems. There is a lack of studies on cytology, histology, morphological variation, yield, and altered restorer backgrounds to identify and develop male sterility markers in cotton hybrids. Hybrid cotton can be efficiently produced by exploiting genetic male sterility. Among the 19 Genetic Male Sterility (GMS) genes discovered, the lines with ms5ms6 genes are mostly utilised to establish successful hybrid cotton in India. Molecular markers closely associated with the MS alleles are identified to facilitate the efficient and rapid backcrossing of male-sterility genes into elite lines or cultivars by marker-assisted backcrossing. The majority of the markers which are random DNA markers (RDMs), are probably lost, when recombination occurs. In contradiction, molecular markers (functional markers, or FMs) within the genic region can be identified and employed in crops for diverse traits, if prospective characteristic genes are known. In this review, the mechanism of male sterility, its gene expression level, and the need for functional markers for the male sterility trait in cotton have been put forward.
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Affiliation(s)
- V Deepa Dharsini
- Department of Genetics and Plant Breeding, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - A Subramanian
- Department of Cotton, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
| | - N Premalatha
- Department of Cotton, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - N Manikanda Boopathi
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - M Djanaguiraman
- Department of Crop Physiology, Directorate of Crop Management, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - V P Santhanakrishnan
- Department of Medicinal and Aromatic Crops, Horticultural College and Research Institute, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Song X, Zhang M, Shahzad K, Zhang X, Guo L, Qi T, Tang H, Wang H, Qiao X, Feng J, Han Y, Xing C, Wu J. Comparative Transcriptome Profiling of CMS-D2 and CMS-D8 Systems Characterizes Fertility Restoration Genes Network in Upland Cotton. Int J Mol Sci 2023; 24:10759. [PMID: 37445936 DOI: 10.3390/ijms241310759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Resolving the genetic basis of fertility restoration for cytoplasmic male sterility (CMS) can improve the efficiency of three-line hybrid breeding. However, the genetic determinants of male fertility restoration in cotton are still largely unknown. This study comprehensively compared the full-length transcripts of CMS-D2 and CMS-D8 systems to identify potential genes linked with fertility restorer genes Rf1 or Rf2. Target comparative analysis revealed a higher percentage of differential genes in each restorer line as compared to their corresponding sterile and maintainer lines. An array of genes with specific expression in the restorer line of CMS-D2 had functional annotations related to floral development and pathway enrichments in various secondary metabolites, while specifically expressed genes in the CMS-D8 restorer line showed functional annotations related to anther development and pathway enrichment in the biosynthesis of secondary metabolites. Further analysis identified potentially key genes located in the target region of fertility restorer genes Rf1 or Rf2. In particular, Ghir_D05G032450 can be the candidate gene related to restorer gene Rf1, and Ghir_D05G035690 can be the candidate gene associated with restorer gene Rf2. Further gene expression validation with qRT-PCR confirmed the accuracy of our results. Our findings provide useful insights into decoding the potential regulatory network that retrieves pollen fertility in cotton and will help to further reveal the differences in the genetic basis of fertility restoration for two CMS systems.
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Affiliation(s)
- Xiatong Song
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Meng Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Kashif Shahzad
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xuexian Zhang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Liping Guo
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Tingxiang Qi
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Huini Tang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hailin Wang
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiuqin Qiao
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Juanjuan Feng
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yang Han
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chaozhu Xing
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jianyong Wu
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China
- National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture and Rural Affairs, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
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Cheng C, Nie H, Li H, Adjibolosoo D, Li B, Jiang K, Cui Y, Zhu M, Zhou B, Guo A, Hua J. Identification of fertility restoration candidate genes from a restorer line R186 for Gossypium harknessii cytoplasmic male sterile cotton. BMC PLANT BIOLOGY 2023; 23:175. [PMID: 37016285 PMCID: PMC10071737 DOI: 10.1186/s12870-023-04185-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The utilization of heterosis based on three-line system is an effective strategy in crop breeding. However, cloning and mechanism elucidation of restorer genes for cytoplasmic male sterility (CMS) in upland cotton have yet been realized. RESULTS This research is based on CMS line 2074A with the cytoplasm from Gossypium harknessii (D2-2) and restorer line R186. The offspring of 2074A × R186 were used to conduct genetic analysis. The fertility mechanism of 2074A can be speculated to be governed by multiple genes, since neither the single gene model nor the double genes model could be used. The bulked segregant analysis (BSA) for (2074A × R186) F2 determined the genetic interval of restorer genes on a region of 4.30 Mb on chromosome D05 that contains 77 annotated genes. Four genes were identified as candidates for fertility restoration using the RNA-seq data of 2074A, 2074B, and R186. There are a number of large effect variants in the four genes between 2074A and R186 that could cause amino acid changes. Evolutionary analysis and identity analysis revealed that GH_D05G3183, GH_D05G3384, and GH_D05G3490 have high identity with their homologs in D2-2, respectively. Tissue differential expression analysis revealed that the genes GH_D05G3183, GH_D05G3384, and GH_D05G3490 were highly expressed in the buds of the line R186. The predicted results demonstrated that GH_D05G3183, GH_D05G3384 and GH_D05G3490 might interact with GH_A02G1295 to regulate orf610a in mitochondria. CONCLUSION Our study uncovered candidate genes for fertility restoration in the restorer line R186 and predicted the possible mechanism for restoring the male fertility in 2074A. This research provided valuable insight into the nucleoplasmic interactions.
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Affiliation(s)
- Cheng Cheng
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Hushuai Nie
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Huijing Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Daniel Adjibolosoo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Bin Li
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Kaiyun Jiang
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Yanan Cui
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Meng Zhu
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Baixue Zhou
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Anhui Guo
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China
| | - Jinping Hua
- Laboratory of Cotton Genetics, Genomics and Breeding /Key Laboratory of Crop Heterosis and Utilization of Ministry of Education, College of Agronomy and Biotechnology, China Agricultural University, Haidian District, No. 2, Yuanmingyuan West Rd, Beijing, 100193, China.
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Zhang T, Xuan L, Mao Y, Hu Y. Cotton heterosis and hybrid cultivar development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:89. [PMID: 37000242 DOI: 10.1007/s00122-023-04334-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/28/2023] [Indexed: 06/19/2023]
Abstract
Cotton, the most important economic crop in the world, displays strong hybrid vigor, and has long been a subject for hybrid cultivar breeding. Here, advances in the theoretical and applied research in cotton heterosis along with its hybrid cultivar development by hand-emasculation and pollination (HEP), cytoplasmic (CMS) and genic male sterile lines (GMS) mainly in China during the past few decades are presented in this review. Three types of hybrids produced by HEP, CMS and GMS facilitating hybrid seed production with hand-pollination have been developed and are being planted simultaneously in cotton production. However, most hybrids commercially planted in production are produced by HEP, therefore, F2 seeds are being extensively planted due to the high cost to produce F1 seed. F2 generations of these combinations exceed the check cultivars in yield usually up to 5~15%. GMS genes (ms2 and ms5ms6) used in hybrid seed production and casual mitochondrial genes for G. harknessii CMS have been cloned. Challenges and opportunities in cotton heterosis and future hybrid cultivar development in cotton are discussed.
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Affiliation(s)
- Tianzhen Zhang
- The Advanced Seed Institute, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Lisha Xuan
- The Advanced Seed Institute, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun Mao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yan Hu
- The Advanced Seed Institute, Plant Precision Breeding Academy, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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Zhang Z, An D, Yu H, Sun L, Cao Y, Zhang B, Wang L. Fine mapping of Rf2, a minor Restorer-of-fertility (Rf) gene for cytoplasmic male sterility in chili pepper G164 (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2699-2709. [PMID: 35710637 DOI: 10.1007/s00122-022-04143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Genome re-sequencing and recombination analyses identified Capana06g000193 as a strong candidate for the minor male fertility restoration locus Rf2 in chili pepper G164 harboring two dominant male fertility restoration genes. Male fertility restoration genes of chili pepper restorer line G164 (Capsicum annuum L.) were studied using molecular marker genotypes of an F2 population (7G) of G164 crossed with the cytoplasmic male sterility line 77013A. The ratio of sterile to fertile single plants in the F2 population was 1:15. This result indicates that chili pepper G164 has two dominant restoration genes, which we designated as Rf1 and Rf2. An individual plant recessive for Rf1 and heterozygous for Rf2, 7G-112 (rf1rf1Rf2rf2), was identified by molecular marker selection and genetic analysis, and a single Rf2 gene-segregating population with a 3:1 ratio of fertile to sterile plants was developed from the self-pollination of male fertile individuals of 77013A and 7G-112 hybrid progeny. Bulk segregant analysis of fertile and sterile pools from the segregating populations was used to genetically map Rf2 to a 3.1-Mb region on chromosome 6. Rf2 was further narrowed to a 179.3-kb interval through recombination analysis of molecular markers and obtained the most likely candidate gene, Capana06g000193.
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Affiliation(s)
- Zhenghai Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Dongliang An
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Hailong Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Liuqing Sun
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Yacong Cao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Baoxi Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China
| | - Lihao Wang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081, China.
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7
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Gao B, Ren G, Wen T, Li H, Zhang X, Lin Z. A super PPR cluster for restoring fertility revealed by genetic mapping, homocap-seq and de novo assembly in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:637-652. [PMID: 34811574 DOI: 10.1007/s00122-021-03990-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Rf candidate genes were related to the super D05_PPR-cluster and verified to be individually nonfunctional. Restorer of fertility (Rf) genes of cytoplasmic male sterility (CMS) is commonly found to be PPR (pentatricopeptide repeat) genes, which are mostly located in a cluster of PPR genes with high similarity. Here, Homocap-seq was applied to analyze PPR clusters in 'three lines,' and we found broad variations within the D05_PPR-cluster in a restorer line and deduced that the D05_PPR-cluster was associated with fertility restoration. Genetic mapping of Rf and Homocap-seq analysis of three genotypes in the F2 population validated that the D05_PPR-cluster was the origin of Rf. Three Rf candidates were cloned that were the most actively expressed genes in the D05_PPR-cluster in the restorer line as revealed by their high-depth amplicons. However, further transgenic experiments showed that none of the candidates could restore fertility of the CMS line independently. Then, the members of the brand-new super D05_PPR-cluster in the restorer line, containing 14 full-length PPRs and at least 13 PPR homologous sequences, were identified by long-read resequencing, which validated the effectiveness of variation and expression prediction of Homocap-seq. Additionally, we found that several PPR duplications, including 2 of the 3 Rf candidates, had undergone site-specific selection as potentially important anther development-associated genes. Finally, we proposed that multiple PPRs were coordinately responsible for the fertility restoration of the CMS line.
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Affiliation(s)
- Bin Gao
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Gaofeng Ren
- Yueyang Institute of Agricultural Science, Yueyang, 414000, Hunan, China
| | - Tianwang Wen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, College of Agronomy, Ministry of Education, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Haiping Li
- Yueyang Institute of Agricultural Science, Yueyang, 414000, Hunan, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences and Technology, Huazhong Agricultural University, Wuhan, Hubei, China.
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Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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Zhang Z, An D, Cao Y, Yu H, Zhu Y, Mei Y, Zhang B, Wang L. Development and application of KASP markers associated with Restorer-of-fertility gene in Capsicum annuum L. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2757-2765. [PMID: 35035134 PMCID: PMC8720122 DOI: 10.1007/s12298-021-01109-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/08/2021] [Accepted: 11/25/2021] [Indexed: 05/09/2023]
Abstract
Fertility restoration of cytoplasmic male sterility (CMS) in Capsicum annuum is controlled by multiple alleles of Restorer-of-fertility (Rf) genes. The isolation of additional Rf genes should therefore enrich the knowledge of CMS/Rf systems and accelerate their exploitation in hybrid seed production. In this study, the fertility restorer gene CaRfm of '0601 M', a non-pungent bell pepper, was genetically mapped to a 1.2-cM region flanked by KASP markers S761 and S183. CaRfm was then physically mapped to a 128.96-Kb interval predicted from 24 recombinants with two co-segregated markers, S423 and S424. CaPPR6 encoding a pentatricopeptide repeat (PPR) protein was suggested as the most likely candidate gene for the CaRfm locus on the basis of sequence alignment as well as genotyping of tightly linked markers. In addition, molecular markers S1597 and S1609, which are immediately adjacent to CaRfm at 15.7 and 57.8-Kb respectively, were developed and applied to marker-assisted selection. The results provided friendly markers for breeding pepper restorer lines and laid the foundation for elucidating the male fertility restoration mechanism. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01109-9.
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Affiliation(s)
- Zhenghai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Dongliang An
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yacong Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Hailong Yu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yanshu Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Yajie Mei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Baoxi Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
| | - Lihao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie, Beijing, 100081 China
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Li T, Zhang X, Guo L, Qi T, Tang H, Wang H, Qiao X, Zhang M, Zhang B, Feng J, Zuo Z, Zhang Y, Xing C, Wu J. Single-molecule real-time transcript sequencing of developing cotton anthers facilitates genome annotation and fertility restoration candidate gene discovery. Genomics 2021; 113:4245-4253. [PMID: 34793949 DOI: 10.1016/j.ygeno.2021.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 07/04/2021] [Accepted: 11/10/2021] [Indexed: 01/23/2023]
Abstract
Heterosis refers to the superior phenotypes observed in hybrids. Cytoplasmic male sterility (CMS) system plays an important role in cotton heterosis utilization. However, the global gene expression patterns of CMS-D2 and its interaction with the restorer gene Rf1 remain unclear. Here, the full-length transcript sequencing was performed in anthers of the CMS-D2 restorer line using PacBio single-molecule real-time sequencing technology. Combining PacBio SMRT long-read isoforms and Illumina RNA-seq data, 107,066 isoforms from 44,338 loci were obtained, including 10,086 novel isoforms of novel genes and 66,419 new isoforms of known genes. Totally 56,572 alternative splicing (AS) events, 1146 lncRNAs, 61 fusion transcripts and 10,466 genes exhibited alternative polyadenylation (APA), and 60,995 novel isoforms with predicted open reading frames (ORFs) were further identified. Furthermore, the specifically expressed genes in restorer line were selected and confirmed by qRT-PCR. These findings provide a basis for upland cotton genome annotation and transcriptome research, and will help to reveal the molecular mechanism of interaction between Rf1 and CMS-D2 cytoplasm.
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Affiliation(s)
- Ting Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China.
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China.
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China.
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China.
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China.
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China
| | - Zhidan Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China
| | - Yongjie Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, Henan, China
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China.
| | - Jianyong Wu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou 450000, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang 455000, Henan, China.
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11
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Physical mapping and InDel marker development for the restorer gene Rf 2 in cytoplasmic male sterile CMS-D8 cotton. BMC Genomics 2021; 22:24. [PMID: 33407111 PMCID: PMC7789476 DOI: 10.1186/s12864-020-07342-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Accepted: 12/22/2020] [Indexed: 11/23/2022] Open
Abstract
Background Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton. Methods The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR. Results The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines. Conclusions This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-020-07342-y.
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Chen Z, Zhong W, Chen S, Zhou Y, Ji P, Gong Y, Yang Z, Mao Z, Zhang C, Mu F. TMT-based quantitative proteomics analyses of sterile/fertile anthers from a genic male-sterile line and its maintainer in cotton (Gossypium hirsutum L.). J Proteomics 2020; 232:104026. [PMID: 33127528 DOI: 10.1016/j.jprot.2020.104026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/27/2020] [Accepted: 10/24/2020] [Indexed: 11/19/2022]
Abstract
Genetic male sterility (GMS) in cotton is important for utilization of heterosis. However, the molecular mechanism of GMS is poorly known. In this study, cytological and proteomics analyses of anthers were conducted in three stages (stage 3 to 5) between GMS line (GA18) and its maintainer (GA18M). The cross-section observation revealed that the tapetal layer in stage 3 was thinner in GA18 compared to GA18M, and the tapetum cells did not degrade in stage 4 in GA18, thus providing no material for microspore development. A total of 1952 differentially expressed proteins (DEPs) were identified between GA18 and GA18M anthers. They were annotated to 52 gene ontology (GO) terms and enriched in 115 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, which formed several complex regulator networks, and dozens of important nodes were identified. Moreover, DEPs were also identified between two consecutive stages of GA18 and GA18M, with functional analyses indicating that numerous developmental differences existed between fertile and sterile anthers. The metabolic pathways were significantly altered, including decreased carbohydrate metabolism, ribosome defects, disturbed protein synthesis, disrupted flavonoids synthesis, etc., that may be involved in male sterility. Overall, these results provide genetic resources that help decipher the molecular mechanisms behind GMS. SIGNIFICANCE: Male sterility is a common phenomenon in flowering plant species, and plays a role in the application of heterosis. However, the molecular mechanism of it remains to be elucidated. Using cytological and proteomics approaches, we found that the tapetal layer development retardation may be the reason of male sterility, which was different from the delayed degradation described in previous studies. More than one thousand differentially expressed proteins were identified between male sterile line and its maintainer, forming a complex regulatory network, and the key nodes were remarked that could be used as candidate proteins related to male sterility in future study. Dozens of metabolic pathways were significantly altered, among them, ribosome defects was a novel pathway that may be involved in male sterility. These results enhance our understanding of the molecular mechanism governing male sterility and lay a foundation for clone of genes association with male sterility.
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Affiliation(s)
- Zhengjie Chen
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Wenjuan Zhong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Siwei Chen
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Yonghang Zhou
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Peicheng Ji
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Yiyun Gong
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Zehu Yang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Zhengxuan Mao
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Chao Zhang
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China
| | - Fangsheng Mu
- Industrial Crop Research Institute, Sichuan Academy of Agricultural Science, No.159 Huajin Avanue, Qingbaijiang District, Chengdu 610300, China.
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13
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Development and utilization of an InDel marker linked to the fertility restorer genes of CMS-D8 and CMS-D2 in cotton. Mol Biol Rep 2020; 47:1275-1282. [PMID: 31894465 DOI: 10.1007/s11033-019-05240-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/17/2019] [Indexed: 01/12/2023]
Abstract
The cytoplasmic male sterility (CMS) system is a useful tool for commercial hybrid cotton seed production. Two main CMS systems, CMS-D8 and CMS-D2, have been recognized with Rf2 and Rf1 as the restorer genes, respectively. The development of molecular markers tightly linked with restorer genes can facilitate the breeding of restorer lines. In this study, the InDel-1892 marker was developed to distinguish Rf2 and Rf1 simultaneously. Sequence alignment implied that CMS-D8-Rf2 has a 32 bp insertion and that CMS-D2-Rf1 has a 186 bp insertion at the InDel-1892 locus. The codominant marker was co-segregated with Rf1 and Rf2. Hence, this marker can be used for tracing Rf1 and Rf2 simultaneously and identifying the allele status at the restorer gene locus. The results of this study will facilitate efficient marker-assisted selection for restorer lines and hybrids of CMS systems.
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14
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Zhao N, Wang Y, Hua J. Genomewide identification of PPR gene family and prediction analysis on restorer gene in Gossypium. J Genet 2018. [DOI: 10.1007/s12041-018-0993-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Zhao C, Zhao G, Geng Z, Wang Z, Wang K, Liu S, Zhang H, Guo B, Geng J. Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton. BMC Genomics 2018; 19:6. [PMID: 29295711 PMCID: PMC5751606 DOI: 10.1186/s12864-017-4406-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/20/2017] [Indexed: 12/04/2022] Open
Abstract
Background Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. The current study combined the bulked segregant analysis (BSA) with SLAF-seq to identify the candidate genes associated with fertility restorer gene (Rf) in CMS cotton. Methods Illumina sequencing systematically investigated the parents. A segregating population comprising of 30 + 30 F2 individuals was developed using 3096A (female parent) as sterile and 866R (male parent) as a restorer. The original data obtained by dual-index sequencing were analyzed to obtain the reads of each sample that were compared to the reference genome in order to identify the SLAF tag with a polymorphism in parent lines and the SNP with read-associated coverage. Based on SLAF tags, SNP-index analysis, Euclidean distance (ED) correlation analysis, and whole genome resequencing, the hot regions were annotated. Results A total of 165,007 high-quality SLAF tags, with an average depth of 47.90× in the parents and 50.78× in F2 individuals, were sequenced. In addition, a total of 137,741 SNPs were detected: 113,311 and 98,861 SNPs in the male and female parent, respectively. A correlation analysis by SNP-index and ED initially located the candidate gene on 1.35 Mb of chrD05, and 20 candidate genes were identified. These genes were involved in genetic variations, single base mutations, insertions, and deletions. Moreover, 42 InDel markers of the whole genome resequencing were also detected. Conclusions In this study, associated markers identified by super-BSA could accelerate the study of CMS in cotton, and as well as in other crops. Some of the 20 genes’ preliminary characteristics provided useful information for further studies on CMS crops. Electronic supplementary material The online version of this article (10.1186/s12864-017-4406-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cunpeng Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Zhaoxiao Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Kaihui Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Suen Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Hanshuang Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Baosheng Guo
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China.
| | - Junyi Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China.
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16
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Wu J, Zhang M, Zhang B, Zhang X, Guo L, Qi T, Wang H, Zhang J, Xing C. Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton. BMC Genomics 2017; 18:454. [PMID: 28595569 PMCID: PMC5465541 DOI: 10.1186/s12864-017-3841-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/02/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Cytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum). The male sterility of CMS-D2 (i.e., A line) can be restored to fertility by a restorer (i.e., R line) carrying the restorer gene Rf1 transferred from the D2 nuclear genome. However, the molecular mechanisms of CMS-D2 and its restoration are poorly understood. RESULTS In this study, a genome-wide comparative transcriptome analysis was performed to identify differentially expressed genes (DEGs) in flower buds among the isogenic fertile R line and sterile A line derived from a backcross population (BC8F1) and the recurrent parent, i.e., the maintainer (B line). A total of 1464 DEGs were identified among the three isogenic lines, and the Rf1-carrying Chr_D05 and its homeologous Chr_A05 had more DEGs than other chromosomes. The results of GO and KEGG enrichment analysis showed differences in circadian rhythm between the fertile and sterile lines. Eleven DEGs were selected for validation using qRT-PCR, confirming the accuracy of the RNA-seq results. CONCLUSIONS Through genome-wide comparative transcriptome analysis, the differential expression profiles of CMS-D2 and its maintainer and restorer lines in Upland cotton were identified. Our results provide an important foundation for further studies into the molecular mechanisms of the interactions between the restorer gene Rf1 and the CMS-D2 cytoplasm.
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Affiliation(s)
- Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003 USA
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 China
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Comprehensive cytological characterization of the Gossypium hirsutum genome based on the development of a set of chromosome cytological markers. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.04.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Lv Y, Ma D, Liang W, Lv Y, Guo W, Hu Y, Zhang T. Construction of BAC contig maps of homoeologous chromosomes A12 and D12 of Gossypium hirsutum L. acc. TM-1. Mol Cytogenet 2015. [PMID: 26221184 PMCID: PMC4517413 DOI: 10.1186/s13039-015-0158-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background The Gossypium hirsutum homoeologous chromosome 12 encodes important genes that contribute to fiber fuzz, lethality, gland development and male sterility. In this study a physical map of the cotton TM-1 chromosome 12 was constructed. A number of large-insert cotton genome libraries are available, and genome-wide physical mapping using large insert segments combined with bacterial cloning is a thriving area of genome research. However, sequencing of the cotton genome is difficult due to sequence repeats and homoeologous regions. In order to effectively distinguish the homologous segments, a new method for adjusting the parameters of the FPC software was applied for contig map construction. Results All available markers on chromosomes A12 and D12 were used to screen the TM-1 BAC library by PCR. A total of 775 clones (387 for A12, 388 for D12) were obtained using Hind III fingerprinting and used for construction of the contig map. Seven pairs of SSR markers located on A12 and D12 were chosen for contig analysis. Following optimization of the tolerance (10) and cutoff (1e-12) parameters, combining all clones from A12 and D12 produced two separate contigs. Conclusions The BAC contig map of chromosomes A12 and D12 was constructed and FPC software parameters were optimized for analysis. The resulting approach is a powerful platform for genome-wide and evolutionary research on cotton.
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Affiliation(s)
- Yanhui Lv
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Dan Ma
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wenhua Liang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yuanda Lv
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Yan Hu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, MOE, Nanjing Agricultural University, Nanjing, 210095 China
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Chen W, Yao J, Chu L, Yuan Z, Li Y, Zhang Y. Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:539-47. [PMID: 25575840 DOI: 10.1007/s00122-014-2452-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Accepted: 12/24/2014] [Indexed: 05/21/2023]
Abstract
Using bulked segregant analysis based on next-generation sequencing, the recessive nulliplex-branch gene was mapped between two SNP markers ~600 kb apart. In a "nulliplex-branch" cotton mutant, most of the flowers arise directly from leaf axils on the main shoot, which usually does not have a fruiting branch. A nulliplex-branch is a useful trait by which to study cotton architecture; however, the genetic basis of this mutant has remained elusive. In this study, bulked segregant analysis combined with next-generation sequencing technology was used to finely map the underlying genes that result in a nulliplex-branch plant. The nulliplex-branch Pima cotton variety, Xinhai-18, was crossed with the normal branch upland cotton line, TM-1, resulting in an F2 population. The nulliplex-branch trait was found to be controlled by the recessive gene gb_nb1. Allelic single-nucleotide polymorphisms (SNPs) were discovered by reduced-representation sequencing between the parents, and their profiles were also characterized in the nulliplex-branch and normal branch bulks constructed using the F2 plants. A candidate ~9.0 Mb-long region comprising 42 SNP markers was found to be associated with gb_nb1, which helped localize it at the ~600-kb interval on Chr 16 by segregation analysis in the F2 population. The closely linked markers with gb_nb1 developed in this study will facilitate the marker-assisted selection of the nulliplex-branch trait, and the fine map constructed will accelerate map-based cloning of gb_nb1.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, The Chinese Academy of Agricultural Sciences, Anyang, 455004, China
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20
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Feng X, Keim D, Wanjugi H, Coulibaly I, Fu Y, Schwarz J, Huesgen S, Cho S. Development of molecular markers for genetic male sterility in Gossypium hirsutum. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:141. [PMID: 26074724 PMCID: PMC4458262 DOI: 10.1007/s11032-015-0336-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/26/2015] [Indexed: 05/21/2023]
Abstract
Genetic male sterility (GMS) in cotton mediated by two homozygous recessive genes, ms5ms5 and ms6ms6, is expressed as non-dehiscent anthers and unviable pollen grains. Sequence analysis on ms5 and ms6 loci in Gossypium hirsutum was conducted to reveal genomic variation at these two loci between GMS and wild-type G. hirsutum inbred lines, and sequence polymorphism linked to ms5 on A12 and ms6 on D12 was revealed. A haplotype marker set that consisted of four SNPs targeting both ms5 and ms6 gene regions was developed and validated for association with GMS in cotton. Predictability of GMS phenotype by this haplotype SNP set was over 99 %. GMS haplotype marker set can serve as a high-throughput molecular breeding tool to select GMS individuals and improve hybrid production efficiency.
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Affiliation(s)
- Xuehui Feng
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
| | - Don Keim
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
| | - Humphrey Wanjugi
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
| | - Issa Coulibaly
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
| | - Yan Fu
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
| | - John Schwarz
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
| | - Scott Huesgen
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
| | - Seungho Cho
- Monsanto Company, 800 N. Lindbergh Blvd, St. Louis, MO 63141 USA
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Ma J, Wei H, Liu J, Song M, Pang C, Wang L, Zhang W, Fan S, Yu S. Selection and characterization of a novel photoperiod-sensitive male sterile line in upland cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:608-18. [PMID: 23691935 DOI: 10.1111/jipb.12067] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 05/15/2013] [Indexed: 05/08/2023]
Abstract
Upland cotton (Gossypium hirsutum L.) shows strong heterosis. However, heterosis is not widely utilized owing to the high cost of hybrid seed production. Creation of a photoperiod-sensitive genetic male sterile line could substantially reduce the cost of hybrid seed production in upland cotton. Such a mutant with virescent marker was found by space mutation in near-earth orbit and its traits had been stable after 4 years of selection in Anyang and Sanya, China. This mutant was fertile with an 11-12.5 h photoperiod when the temperature was higher than 21.5 °C and was sterile with a 13-14.5 h photoperiod. Genetic analysis indicated that both traits were controlled by a single recessive gene or two closely linked genes. Also, the cytological observations and transcriptome profiling analysis showed that the degradation of pollen grain cytoplasm should be the primary reason why the mutant line were male sterile under long-day conditions.
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Affiliation(s)
- Jianhui Ma
- State Key Laboratory of Cotton Biology, the Institute of Cotton Research, the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Cai C, Tong X, Liu F, Lv F, Wang H, Zhang T, Guo W. Discovery and identification of a novel Ligon lintless-like mutant (Lix) similar to the Ligon lintless (Li1) in allotetraploid cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:963-70. [PMID: 23397278 DOI: 10.1007/s00122-012-2029-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2011] [Accepted: 12/06/2012] [Indexed: 05/10/2023]
Abstract
Mutants are a powerful resource for studying gene structure, function, and evolution. In this present study, a novel Ligon lintless-like mutant (Lix), that has short fibers and deformed leaves and stems, was isolated from the progeny of transgenic cottons. The Lix mutant is similar in morphology to the Ligon lintless (Li1) mutant. Genetic analysis and molecular mapping were performed for the Lix and Li1 mutants. These two mutants are monogenic dominant mutants with distorted growth of vegetative and reproductive structures. Seedlings of the dominant homozygote Li 1 Li 1 genotype are lethal, while LixLix plants are viable but show no reproductive growth. Molecular tagging showed that the Lix gene is located on Chr. 04 in a 30.9-cM region spanned by NAU8376 and NAU3469. In a previous study, the Li 1 gene was mapped to Chr. 22, and Chr. 04 and Chr. 22 are homoelogous chromosomes in tetraploid cotton. So, we propose that Lix and Li1 mutants have similar mutated morphology, and Lix is mapped to a homoelogous chromosome carrying Li 1 . The identification and genetic mapping of Lix/Li 1 genes using mutants provides a foundation for isolating these genes. In turn, this will permit studies to elucidate the functional and evolutionary roles for these genes in cotton growth and development.
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Affiliation(s)
- Caiping Cai
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, Jiangsu Province, People's Republic of China
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23
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Wang ZW, Wang C, Gao L, Mei SY, Zhou Y, Xiang CP, Wang T. Heterozygous alleles restore male fertility to cytoplasmic male-sterile radish (Raphanus sativus L.): a case of overdominance. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:2041-2048. [PMID: 23630327 PMCID: PMC3638831 DOI: 10.1093/jxb/ert065] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The practice of hybridization has greatly contributed to the increase in crop productivity. A major component that exploits heterosis in crops is the cytoplasmic male sterility (CMS)/nucleus-controlled fertility restoration (Rf) system. Through positional cloning, it is shown that heterozygous alleles (RsRf3-1/RsRf3-2) encoding pentatricopeptide repeat (PPR) proteins are responsible for restoring fertility to cytoplasmic male-sterile radish (Raphanus sativus L.). Furthermore, it was found that heterozygous alleles (RsRf3-1/RsRf3-2) show higher expression and RNA polymerase II occupancy in the CMS cytoplasmic background compared with their homozygous alleles (RsRf3-1/RsRf3-1 or RsRf3-2/RsRf3-2). These data provide new insights into the molecular mechanism of fertility restoration to cytoplasmic male-sterile plants and illustrate a case of overdominance.
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Affiliation(s)
- Zhi Wei Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Chuan Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
- Graduate University of the Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lei Gao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Shi Yong Mei
- Hubei Academy of Agricultural Sciences, Wuhan 430064, PR China
| | - Yuan Zhou
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
| | - Chang Ping Xiang
- Key Laboratory of Ministry of Education for Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, PR China
| | - Ting Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, PR China
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Lv Y, Zhao L, Xu X, Wang L, Wang C, Zhang T, Guo W. Characterization of expressed sequence tags from developing fibers of Gossypium barbadense and evaluation of insertion-deletion variation in tetraploid cultivated cotton species. BMC Genomics 2013; 14:170. [PMID: 23497047 PMCID: PMC3600364 DOI: 10.1186/1471-2164-14-170] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 03/06/2013] [Indexed: 12/21/2022] Open
Abstract
Background Cotton is the leading fiber crop worldwide. Gossypium barbadense is an important species of cotton because of its extra-long staple fibers with superior luster and silkiness. However, a systematic analysis and utilization of cDNA sequences from G. barbadense fiber development remains understudied. Results A total of 21,079 high quality sequences were generated from two non-normalized cDNA libraries prepared by using a mixture of G. barbadense Hai7124 fibers and ovules. After assembly processing, a set of 8,653 unigenes were obtained. Of those, 7,786 were matched to known proteins and 7,316 were assigned to functional categories. The molecular functions of these unigenes were mostly related to binding and catalytic activity, and carbohydrate, amino acid, and energy metabolisms were major contributors among the subsets of metabolism. Sequences comparison between G. barbadense and G. hirsutum revealed that 8,245 unigenes from G. barbadense were detected the similarity with those released publicly in G. hirsutum, however, the remaining 408 sequences had no hits against G. hirsutum unigenes database. Furthermore, 13,275 putative ESTs InDels loci involved in the orthologous and/or homoeologous differences between/within G. barbadense and G. hirsutum were discovered by in silico analyses, and 2,160 InDel markers were developed by ESTs with more than five insertions or deletions. By gel electrophoresis combined with sequencing verification, 71.11% candidate InDel loci were reconfirmed orthologous and/or homoeologous loci polymorphisms using G. hirsutum acc TM-1 and G. barbadense cv Hai7124. Blastx result showed among 2,160 InDel loci, 81 with significant function similarity with known genes associated with secondary wall synthesis process, indicating the important roles in fiber quality in tetraploid cultivated cotton species. Conclusion Sequence comparisons and InDel markers development will lay the groundwork for promoting the identification of genes related to superior agronomic traits, genetic differentiation and comparative genomic studies between G. hirsutum and G. barbadense.
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Affiliation(s)
- Yuanda Lv
- National Key Laboratory of Crop Genetics & Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, China
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A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. G3-GENES GENOMES GENETICS 2012; 2:43-58. [PMID: 22384381 PMCID: PMC3276184 DOI: 10.1534/g3.111.001552] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 11/04/2011] [Indexed: 11/18/2022]
Abstract
Genetic linkage maps play fundamental roles in understanding genome structure, explaining genome formation events during evolution, and discovering the genetic bases of important traits. A high-density cotton (Gossypium spp.) genetic map was developed using representative sets of simple sequence repeat (SSR) and the first public set of single nucleotide polymorphism (SNP) markers to genotype 186 recombinant inbred lines (RILs) derived from an interspecific cross between Gossypium hirsutum L. (TM-1) and G. barbadense L. (3-79). The genetic map comprised 2072 loci (1825 SSRs and 247 SNPs) and covered 3380 centiMorgan (cM) of the cotton genome (AD) with an average marker interval of 1.63 cM. The allotetraploid cotton genome produced equivalent recombination frequencies in its two subgenomes (At and Dt). Of the 2072 loci, 1138 (54.9%) were mapped to 13 At-subgenome chromosomes, covering 1726.8 cM (51.1%), and 934 (45.1%) mapped to 13 Dt-subgenome chromosomes, covering 1653.1 cM (48.9%). The genetically smallest homeologous chromosome pair was Chr. 04 (A04) and 22 (D04), and the largest was Chr. 05 (A05) and 19 (D05). Duplicate loci between and within homeologous chromosomes were identified that facilitate investigations of chromosome translocations. The map augments evidence of reciprocal rearrangement between ancestral forms of Chr. 02 and 03 versus segmental homeologs 14 and 17 as centromeric regions show homeologous between Chr. 02 (A02) and 17 (D02), as well as between Chr. 03 (A03) and 14 (D03). This research represents an important foundation for studies on polyploid cottons, including germplasm characterization, gene discovery, and genome sequence assembly.
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26
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Construction and characterization of a bacterial artificial chromosome library for the A-genome of cotton (G. arboreum L.). J Biomed Biotechnol 2010; 2010. [PMID: 20827418 PMCID: PMC2933907 DOI: 10.1155/2011/457137] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Revised: 06/17/2010] [Accepted: 07/29/2010] [Indexed: 02/03/2023] Open
Abstract
A bacterial artificial chromosome (BAC) library for the A-genome of cotton has been constructed from the leaves of G. arboreum L cv. Jianglinzhongmian. It is used as elite A-genome germplasm resources in the present cotton breeding program and has been used to build a genetic reference map of cotton. The BAC library consists of 123,648 clones stored in 322 384-well plates. Statistical analysis of a set of 103 randomly selected BAC clones indicated that each clone has an average insert length of 100.2 kb per plasmid, with a range of 30 to 190 kb. Theoretically, this represents 7.2 haploid genome equivalents based on an A-genome size of 1697 Mb. The BAC library has been arranged in column pools and superpools allowing screening with various PCR-based markers. In the future, the A-genome cotton BAC library will serve as both a giant gene resource and a valuable tool for map-based gene isolation, physical mapping and comparative genome analysis.
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27
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Inheritance of Fertility Restoration for Cytoplasmic Male Sterility in a New Gossypium barbadense Restorer. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1671-2927(09)60119-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Structure and size variations between 12A and 12D homoeologous chromosomes based on high-resolution cytogenetic map in allotetraploid cotton. Chromosoma 2010; 119:255-66. [PMID: 20127105 DOI: 10.1007/s00412-009-0254-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2009] [Revised: 12/11/2009] [Accepted: 12/21/2009] [Indexed: 10/19/2022]
Abstract
Cotton is a model system for studying polyploidization, genomic organization, and genome-size variation because the allotetraploid was formed 1-2 million years ago, which is old enough for sequence divergence but relatively recent to maintain genome stability. In spite of characterizing random genomic sequences in many polyploidy plants, the cytogenetic and sequence data that decipher homoeologous chromosomes are very limited in allopolyploid species. Here, we reported comprehensive analyses of integrated cytogenetic and linkage maps of homoeologous chromosomes 12A and 12D in allotetraploid cotton using fluorescence in situ hybridization and a large number of bacterial artificial chromosomes that were anchored by simple sequence repeat markers in the corresponding linkage maps. Integration of genetic loci into physical localizations showed considerable variation of genome organization, structure, and size between 12A and 12D homoeologous chromosomes. The distal regions of the chromosomes displayed relatively lower levels of structural and size variation than other regions of the chromosomes. The highest level of variation was found in the pericentric regions in the long arms of the two homoeologous chromosomes. The genome-size difference between A and D sub-genomes in allotetraploid cotton was mainly associated with uneven expansion or contraction between different regions of homoeologous chromosomes. As an attempt for studying on the polyploidy homoeologous chromosomes, these results are of general interest to the understanding and future sequencing of complex genomes in plant species.
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Wang K, Yang Z, Shu C, Hu J, Lin Q, Zhang W, Guo W, Zhang T. Higher axial-resolution and sensitivity pachytene fluorescence in situ hybridization protocol in tetraploid cotton. Chromosome Res 2009; 17:1041-50. [PMID: 19844799 DOI: 10.1007/s10577-009-9085-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 09/30/2009] [Indexed: 11/24/2022]
Abstract
Fluorescence in situ hybridization (FISH) based on pachytene chromosomes has become an important cytogenetic tool to construct high axial-resolution and sensitivity cytogenetic maps. However, the application of this technique in cotton has lagged behind due to difficulties in chromosome preparation. To date, successful FISH based on cotton pachytene chromosomes has not been reported. In this study, the first protocol developed for pachytene chromosome preparation in tetraploid cotton is presented. This protocol yielded chromosome spreads suitable for large and small DNA probe FISH labeling. Two important parameters, axial-resolution and sensitivity, of FISH on mitotic metaphase and pachytene chromosomes were systematically analyzed. The results demonstrated that DNA targets separated by 0.6 cM and low-copy targets as small as 3-kb were resolved and detected, respectively, in pachytene FISH. The application of our FISH protocol will continue to improve and provide a point of departure for constructing an integrated high axial-resolution cytogenetic map in cotton.
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Affiliation(s)
- Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
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Completely distinguishing individual A-genome chromosomes and their karyotyping analysis by multiple bacterial artificial chromosome - fluorescence in situ hybridization. Genetics 2008; 178:1117-22. [PMID: 18287408 DOI: 10.1534/genetics.107.083576] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Twenty bacterial artificial chromosome (BAC) clones that could produce bright signals and no or very low fluorescence in situ hybridization (FISH) background were identified from Gossypium arboreum cv. JLZM, and G. hirsutum accession (acc.) TM-1 and 0-613-2R. Combining with 45S and 5S rDNA, a 22-probe cocktail that could identify all 13 G. arboreum chromosomes simultaneously was developed. According to their homology with tetraploid cotton, the G. arboreum chromosomes were designated as A1-A13, and a standard karyotype analysis of G. arboreum was presented. These results demonstrated an application for multiple BAC-FISH in cotton cytogenetic studies and a technique to overcome the problem of simultaneous chromosome recognition in mitotic cotton cells.
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31
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Xiang H, Li M, Yang F, Guo Q, Zhan S, Lin H, Miao X, Huang Y. Fine mapping of E(kp)-1, a locus associated with silkworm (Bombyx mori) proleg development. Heredity (Edinb) 2008; 100:533-40. [PMID: 18364737 DOI: 10.1038/hdy.2008.10] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The silkworm homeotic mutant E(kp) has a pair of rudimentary abdominal legs, called prolegs, in its A2 segment. This phenotype is caused by a single dominant mutation at the E(kp)-1 locus, which was previously mapped to chromosome 6. To explore the possible association of Hox genes with proleg development in the silkworm, a map-based cloning strategy was used to isolate the E(kp)-1 locus. Five E(kp)-1-linked simple sequence repeat markers on chromosome 6 were used to generate a low-resolution map with a total genetic distance of 39.5 cM. Four additional cleaved amplified polymorphic sequence markers were developed based on the initial map. The closest marker to E(kp)-1 was at a genetic distance of 2.7 cM. A high-resolution genetic map was constructed using nine BC1 segregating populations consisting of 2396 individuals. Recombination suppression was observed in the vicinity of E(kp)-1. Four molecular markers were tightly linked to E(kp)-1, and three were clustered with it. These markers were used to screen a BAC library. A single bacterial artificial chromosome (BAC) clone spanning the E(kp)-1 locus was identified, and E(kp)-1 was delimited to a region less than 220 kb long that included the Hox gene abdominal-A and a non-coding locus, iab-4. These results provide essential information for the isolation of this locus, which may shed light on the mechanism of proleg development in the silkworm and possibly in Lepidoptera.
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Affiliation(s)
- H Xiang
- Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Center of Insect Science, The Chinese Academy of Sciences, Shanghai, P.R. China
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Wang F, Stewart JM, Zhang J. Molecular markers linked to the Rf2 fertility restorer gene in cotton. Genome 2008; 50:818-24. [PMID: 17893722 DOI: 10.1139/g07-061] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Cytoplasmic male sterility (CMS) is a maternally inherited trait in which plants do not produce viable pollen. Fertility in plants with CMS can be recovered by nuclear restorer genes. Most restorer genes cloned so far are members of the pentatricopeptide repeat (PPR) protein family. The objective of our study was to use the CMS-D8 and restoration (Rf2) system of cotton (Gossypium hirsutum L.) to develop more DNA markers for the Rf2 gene. In a backcross population with 112 plants, segregation of male fertility was 1 fertile : 1 sterile. Three new RAPD markers were identified for Rf2, one of which was converted to a CAPS marker. In addition, 2 AFLP markers and 1 SSR marker were identified to be linked to the fertility restorer gene (Rf2). PPR motif primers were designed based on the conserved PPR motifs and used in combination with AFLP primers to test the mapping population, and 1 PPR-AFLP marker was identified. A linkage map with 9 flanking markers including 1 from a previous study was constructed.
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Affiliation(s)
- Fei Wang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
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Chen ZJ, Scheffler BE, Dennis E, Triplett BA, Zhang T, Guo W, Chen X, Stelly DM, Rabinowicz PD, Town CD, Arioli T, Brubaker C, Cantrell RG, Lacape JM, Ulloa M, Chee P, Gingle AR, Haigler CH, Percy R, Saha S, Wilkins T, Wright RJ, Van Deynze A, Zhu Y, Yu S, Abdurakhmonov I, Katageri I, Kumar PA, Mehboob-Ur-Rahman, Zafar Y, Yu JZ, Kohel RJ, Wendel JF, Paterson AH. Toward sequencing cotton (Gossypium) genomes. PLANT PHYSIOLOGY 2007; 145:1303-1310. [PMID: 18056866 PMCID: PMC2151711 DOI: 10.1104/pp.107.107672] [Citation(s) in RCA: 282] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Accepted: 09/10/2007] [Indexed: 02/05/2023]
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Yip PY, Chau CF, Mak CY, Kwan HS. DNA methods for identification of Chinese medicinal materials. Chin Med 2007; 2:9. [PMID: 17803808 PMCID: PMC2042497 DOI: 10.1186/1749-8546-2-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2006] [Accepted: 09/05/2007] [Indexed: 11/10/2022] Open
Abstract
As adulterated and substituted Chinese medicinal materials are common in the market, therapeutic effectiveness of such materials cannot be guaranteed. Identification at species-, strain- and locality-levels, therefore, is required for quality assurance/control of Chinese medicine. This review provides an informative introduction to DNA methods for authentication of Chinese medicinal materials. Technical features and examples of the methods based on sequencing, hybridization and polymerase chain reaction (PCR) are described and their suitability for different identification objectives is discussed.
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Affiliation(s)
- Pui Ying Yip
- Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Chi Fai Chau
- Department of Food Science and Biotechnology, National Chung Hsing University, 250 Kuokuang Road, Taichung 40227, Taiwan
| | - Chun Yin Mak
- Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Hoi Shan Kwan
- Department of Biology, The Chinese University of Hong Kong, Shatin, Hong Kong
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Wang K, Guo W, Zhang T. Development of one set of chromosome-specific microsatellite-containing BACs and their physical mapping in Gossypium hirsutum L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:675-82. [PMID: 17632699 DOI: 10.1007/s00122-007-0598-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2006] [Accepted: 06/17/2007] [Indexed: 05/16/2023]
Abstract
Fluorescence in situ hybridization (FISH), using bacterial artificial chromosome (BAC) clone as probe, is a reliable cytological technique for chromosome identification. It has been used in many plants, especially in those containing numerous small chromosomes. We previously developed eight chromosome-specific BAC clones from tetraploid cotton, which were used as excellent cytological markers for chromosomes identification. Here, we isolated the other chromosome-specific BAC clones to make a complete set for the identification of all 26 chromosome-pairs by this technology in tetraploid cotton (Gossypium hirsutum L.). This set of BAC markers was demonstrated to be useful to assign each chromosome to a genetic linkage group unambiguously. In addition, these BAC clones also served as convenient and reliable landmarks for establishing physical linkage with unknown targeted sequences. Moreover, one BAC containing an EST, with high sequence similarity to a G. hirsutum ethylene-responsive element-binding factor was located physically on the long arm of chromosome A7 with the help of a chromosome-A7-specific BAC FISH marker. Comparative analysis of physical marker positions in the chromosomes by BAC-FISH and genetic linkage maps demonstrated that most of the 26 BAC clones were localized close to or at the ends of their respective chromosomes, and indicated that the recombination active regions of cotton chromosomes are primarily located in the distal regions. This technology also enables us to make associations between chromosomes and their genetic linkage groups and re-assign each chromosome according to the corresponding genetic linkage group. This BAC clones and BAC-FISH technology will be useful for us to evaluate grossly the degree to which a linkage map provides adequate coverage for developing a saturated genetic map, and provides a powerful resource for cotton genomic researches.
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Affiliation(s)
- Kai Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
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