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Niu H, Kuang M, Huang L, Shang H, Yuan Y, Ge Q. Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60. BMC PLANT BIOLOGY 2023; 23:179. [PMID: 37020180 PMCID: PMC10074700 DOI: 10.1186/s12870-023-04147-5] [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: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield. RESULTS Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation. CONCLUSIONS A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Kuang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Longyu Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Mir S, Sakina A, Masoodi KZ, Bhat KM, Padder BA, Murtaza I, Nazir N, Bhat ZA, Wani SH, Shikari AB. Mapping of quantitative trait loci for scab resistance in apple (Malus × domestica) variety, Shireen. Mol Biol Rep 2022; 49:5555-5566. [PMID: 35579736 DOI: 10.1007/s11033-022-07488-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 04/19/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Scab caused by Venturia inaequalis (Cke.) Wint. is the most important fungal disease of apple. Fungicide application is a widely practiced method of disease control. However, the use of chemicals is costintensive, tedious, and ecologically unsafe. The development of genetic resistance and the breeding of resistant cultivars is the most reliable and safest option. One such source of scab resistance happens to be the variety 'Shireen', released from SKUAST-Kashmir. However, to date, the nature of resistance and its genetic control have not been characterized. Objective This research aimed to elucidate the genetic basis of scab resistance in Shireen. METHODS Genetic mapping of quantitative trait loci (QTL) for resistance to apple scab disease was performed using an F1 cross developed between the susceptible cultivar 'StarKrimson' and the resistant cultivar 'Shireen'. The population was evaluated for two consecutive years. Further, six candidate genes were analyzed via quantitative real-time PCR, to determine their expression level in response to the pathogen infestation. RESULTS Genotyping and disease phenotyping of populations led us to identify two quantitative trait loci (QTLs), namely qRVI.SS-LG2.2019 and qRVI.SS-LG8.2019 on chromosomes 2 and 8 with LOD-values of 7.67 and 4.99 respectively, and six potential CDGs for the polygenic resistance in 'Shireen'. The genomic region corresponding to the mapped QTLs in LG 2 and LG 8 of 'Shireen' was examined for candidate genes possibly related to scab resistance using in silico analysis. CONCLUSION The QTLs mapped in the genetic background of Shireen are the novel QTLs and may be transferred to desirable genetic backgrounds and provide opportunities for isolation and cloning of genes apart from their utility to achieve durable resistance to scab.
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Affiliation(s)
- Saba Mir
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Aafreen Sakina
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Khalid Z Masoodi
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Khalid M Bhat
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Bilal A Padder
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Imtiyaz Murtaza
- Division of Basic Sciences and Humanities, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Nagina Nazir
- Division of Agricultural Statistics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Zahoor Ahmad Bhat
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Shalimar, Srinagar, J&K, 190025, India
| | - Shabir H Wani
- MRCFC, KhudwaniSher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, J&K, 190025, India.
| | - Asif B Shikari
- MRCFC, KhudwaniSher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir (SKUAST-K), Srinagar, J&K, 190025, India.
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Niu H, Ge Q, Shang H, Yuan Y. Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton. Front Genet 2022; 13:855574. [PMID: 35450216 PMCID: PMC9016478 DOI: 10.3389/fgene.2022.855574] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
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Yu D, Gu X, Zhang S, Dong S, Miao H, Gebretsadik K, Bo K. Molecular basis of heterosis and related breeding strategies reveal its importance in vegetable breeding. HORTICULTURE RESEARCH 2021; 8:120. [PMID: 34059656 PMCID: PMC8166827 DOI: 10.1038/s41438-021-00552-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 03/07/2021] [Accepted: 03/22/2021] [Indexed: 05/02/2023]
Abstract
Heterosis has historically been exploited in plants; however, its underlying genetic mechanisms and molecular basis remain elusive. In recent years, due to advances in molecular biotechnology at the genome, transcriptome, proteome, and epigenome levels, the study of heterosis in vegetables has made significant progress. Here, we present an extensive literature review on the genetic and epigenetic regulation of heterosis in vegetables. We summarize six hypotheses to explain the mechanism by which genes regulate heterosis, improve upon a possible model of heterosis that is triggered by epigenetics, and analyze previous studies on quantitative trait locus effects and gene actions related to heterosis based on analyses of differential gene expression in vegetables. We also discuss the contributions of yield-related traits, including flower, fruit, and plant architecture traits, during heterosis development in vegetables (e.g., cabbage, cucumber, and tomato). More importantly, we propose a comprehensive breeding strategy based on heterosis studies in vegetables and crop plants. The description of the strategy details how to obtain F1 hybrids that exhibit heterosis based on heterosis prediction, how to obtain elite lines based on molecular biotechnology, and how to maintain heterosis by diploid seed breeding and the selection of hybrid simulation lines that are suitable for heterosis research and utilization in vegetables. Finally, we briefly provide suggestions and perspectives on the role of heterosis in the future of vegetable breeding.
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Affiliation(s)
- Daoliang Yu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingfang Gu
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shengping Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shaoyun Dong
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Han Miao
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Kiros Gebretsadik
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
- Department of Plant Science, Aksum University, Shire Campus, Shire, Ethiopia
| | - Kailiang Bo
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China.
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Liu J, Li M, Zhang Q, Wei X, Huang X. Exploring the molecular basis of heterosis for plant breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:287-298. [PMID: 30916464 DOI: 10.1111/jipb.12804] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 03/13/2019] [Indexed: 05/18/2023]
Abstract
Since approximate a century ago, many hybrid crops have been continually developed by crossing two inbred varieties. Owing to heterosis (hybrid vigor) in plants, these hybrids often have superior agricultural performances in yield or disease resistance succeeding their inbred parental lines. Several classical hypotheses have been proposed to explain the genetic causes of heterosis. During recent years, many new genetics and genomics strategies have been developed and used for the identifications of heterotic genes in plants. Heterotic effects of the heterotic loci and molecular functions of the heterotic genes are being investigated in many plants such as rice, maize, sorghum, Arabidopsis and tomato. More and more data and knowledge coming from the molecular studies of heterotic loci and genes will serve as a valuable resource for hybrid breeding by molecular design in future. This review aims to address recent advances in our understanding of the genetic and molecular mechanisms of heterosis in plants. The remaining scientific questions on the molecular basis of heterosis and the potential applications in breeding are also proposed and discussed.
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Affiliation(s)
- Jie Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Mengjie Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Qi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xin Wei
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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Li C, Yu H, Li C, Zhao T, Dong Y, Deng X, Hu J, Zhang Y, Zhang F, Daud MK, Chen J, Zhu S. QTL Mapping and Heterosis Analysis for Fiber Quality Traits Across Multiple Genetic Populations and Environments in Upland Cotton. FRONTIERS IN PLANT SCIENCE 2018; 9:1364. [PMID: 30374360 PMCID: PMC6196769 DOI: 10.3389/fpls.2018.01364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2018] [Accepted: 08/28/2018] [Indexed: 05/03/2023]
Abstract
An "immortalized F2" (IF2) population and two reciprocal backcross (HSBCF1 and MARBCF1) populations were constructed to investigate the genetic bases of fiber quality traits in upland cotton across four different environments. A relatively high level of heterosis for micronaire (MIC) in IF2 population as well as fiber length (FL) and MIC in MARBCF1 population was observed. A total of 167 quantitative trait loci (QTLs) were detected in the three related experimental populations and their corresponding midparental heterosis (MPH) datasets using the composite interval mapping (CIM) approach. An analysis of genetic effects of QTLs detected in different populations and their MPH datasets showed 16 (24.24%) QTLs of partial dominance, and 46 (69.70%) QTLs of overdominance were identified in an IF2 population; 89 (62.68%) additive QTLs, three (2.11%) partial dominant QTLs, and 49 (34.51%) over-dominant QTLs were detected in two BCF1 populations. Multi-environment analysis showed 48 and 56 main-QTLs (m-QTLs) and 132 and 182 epistasis-QTLs (e-QTLs), by inclusive composite interval mapping (ICIM) in IF2 and two BCF1 populations, respectively. Phenotypic variance explained by e-QTLs, except for MARBCF1 population, was higher than that by m-QTLs. Thus, the overdominant, partial dominant, and epistasis effects were the main causes of heterosis in the IF2 population, whereas the additive, overdominant, and epistasis effects were the primary genetic basis of heterosis in the two BCF1 populations. Altogether, additive effect, partial dominance, overdominance, and epistasis contributed to fiber quality heterosis in upland cotton, but overdominance and epistasis were the most important factors.
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Affiliation(s)
- Cong Li
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Hurong Yu
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Cheng Li
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Tianlun Zhao
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Yating Dong
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Xiaolei Deng
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Jiahui Hu
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Yi Zhang
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Fan Zhang
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - M. K. Daud
- Department of Agronomy, Zhejiang University, Hangzhou, China
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology, Kohat, Pakistan
| | - Jinhong Chen
- Department of Agronomy, Zhejiang University, Hangzhou, China
| | - Shuijin Zhu
- Department of Agronomy, Zhejiang University, Hangzhou, China
- *Correspondence: Shuijin Zhu
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Differential transcript profiling alters regulatory gene expression during the development of Gossypium arboreum, G.stocksii and somatic hybrids. Sci Rep 2017; 7:3120. [PMID: 28600526 PMCID: PMC5466607 DOI: 10.1038/s41598-017-03431-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 05/02/2017] [Indexed: 11/20/2022] Open
Abstract
Polyploidy or genome doubling (i.e., the presence of two or more diploid parental genome sets within an organism) are very important in higher plants. Of particular interest are the mechanisms in the new microenvironment of the common nucleus, where doubled regulatory networks interact to generate a viable genetic system capable of regulating growth, development and responses to the environment. To determine the effects of whole genome merging and doubling on the global gene expression architecture of a new polyploid, derived from protoplast fusion of the A1A1 genome of Gossypium arboreum and the E1E1 genome of Gossypium stocksii, we monitored gene expression through cDNA-AFLP in the somatic hybrids (G. arboreum + G. stocksii). The genomic expression patterns of the somatic hybrids revealed that changes in expression levels mainly involved regulatory genes (31.8% of the gene expression profiles), and the AA and EE genomes contributed equally to genome-wide expression in the newly formed AAEE genome from additivity and dominance effects. These results provide a novel perspective on polyploid gene regulation and hint at the underlying genetic basis of allopolyploid adaption in the new microenvironmental nucleus.
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Liu C, Yuan D, Lin Z. Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. J Genet 2015; 93:689-97. [PMID: 25572227 DOI: 10.1007/s12041-014-0425-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantitative trait locus (QTL) mapping is an important method in marker-assisted selection breeding. Many studies on the QTLs focus on cotton fibre yield and quality; however, most are conducted at the DNA level, which may reveal null QTLs. Hence, QTL mapping based on transcriptome maps at the cDNA level is often more reliable. In this study, an interspecific transcriptome map of allotetraploid cotton was developed based on an F2 population (Emian22 x 3-79) by amplifying cDNA using EST-SSRs. The map was constructed using cDNA obtained from developing fibres at five days post anthesis (DPA). A total of 1270 EST-SSRs were screened for polymorphisms between the mapping parents. The resulting transcriptome linkage map contained 242 markers that were distributed in 32 linkage groups (26 chromosomes). The full length of this map is 1938.72 cM with a mean marker distance of 8.01 cM. The functions of some ESTs have been annotated by exploring homologous sequences. Some markers were related to the differentiation and elongation of cotton fibre, while most were related to the basic metabolism. This study demonstrates that constructing a transcriptome linkage map by amplifying cDNAs using EST-SSRs is a simple and practical method as well as a powerful tool to map eQTLs for fibre quality and other traits in cotton.
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Affiliation(s)
- Chuanxiang Liu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, Hubei, People's Republic of China.
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Wang Q, Fang L, Chen J, Hu Y, Si Z, Wang S, Chang L, Guo W, Zhang T. Genome-wide mining, characterization, and development of microsatellite markers in gossypium species. Sci Rep 2015; 5:10638. [PMID: 26030481 PMCID: PMC4650602 DOI: 10.1038/srep10638] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 05/01/2015] [Indexed: 12/02/2022] Open
Abstract
Although much research has been conducted to characterize microsatellites and develop markers, the distribution of microsatellites remains ambiguous and the use of microsatellite markers in genomic studies and marker-assisted selection is limited. To identify microsatellites for cotton research, we mined 100,290, 83,160, and 56,937 microsatellites with frequencies of 41.2, 49.1, and 74.8 microsatellites per Mb in the recently sequenced Gossypium species: G. hirsutum, G. arboreum, and G. raimondii, respectively. The distributions of microsatellites in their genomes were non-random and were positively and negatively correlated with genes and transposable elements, respectively. Of the 77,996 developed microsatellite markers, 65,498 were physically anchored to the 26 chromosomes of G. hirsutum with an average marker density of 34 markers per Mb. We confirmed 67,880 (87%) universal and 7,705 (9.9%) new genic microsatellite markers. The polymorphism was estimated in above three species by in silico PCR and validated with 505 markers in G. hirsutum. We further predicted 8,825 polymorphic microsatellite markers within G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124. In our study, genome-wide mining and characterization of microsatellites, and marker development were very useful for the saturation of the allotetraploid genetic linkage map, genome evolution studies and comparative genome mapping.
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Affiliation(s)
- Qiong Wang
- 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China [2]
| | - Lei Fang
- 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China [2]
| | - Jiedan Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Hu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Zhanfeng Si
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Sen Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Lijing Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R &D Engineering Center (the Ministry of Education), Nanjing Agricultural University, Nanjing 210095, China
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Deciphering the ability of Agaricus bisporus var. burnettii to produce mushrooms at high temperature (25°C). Fungal Genet Biol 2014; 73:1-11. [DOI: 10.1016/j.fgb.2014.08.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/18/2014] [Accepted: 08/31/2014] [Indexed: 01/02/2023]
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Guo T, Yang N, Tong H, Pan Q, Yang X, Tang J, Wang J, Li J, Yan J. Genetic basis of grain yield heterosis in an "immortalized F₂" maize population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2149-58. [PMID: 25104328 DOI: 10.1007/s00122-014-2368-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2013] [Accepted: 07/19/2014] [Indexed: 05/04/2023]
Abstract
Genetic basis of grain yield heterosis relies on the cumulative effects of dominance, overdominance, and epistasis in maize hybrid Yuyu22. Heterosis, i.e., when F1 hybrid phenotypes are superior to those of the parents, continues to play a critical role in boosting global grain yield. Notwithstanding our limited insight into the genetic and molecular basis of heterosis, it has been exploited extensively using different breeding approaches. In this study, we investigated the genetic underpinnings of grain yield and its components using "immortalized F2" and recombinant inbred line populations derived from the elite hybrid Yuyu22. A high-density linkage map consisting of 3,184 bins was used to assess (1) the additive and additive-by-additive effects determined using recombinant inbred lines; (2) the dominance and dominance-by-dominance effects from a mid-parent heterosis dataset; and (3) the various genetic effects in the "immortalized F2" population. Compared with a low-density simple sequence repeat map, the bin map identified more quantitative trait loci, with higher LOD scores and better accuracy of detecting quantitative trait loci. The bin map showed that, among all traits, dominance was more important to heterosis than other genetic effects. The importance of overdominance/pseudo-overdominance was proportional to the amount of heterosis. In addition, epistasis contributed to heterosis as well. Phenotypic variances explained by the QTLs detected were close to the broad-sense heritabilities of the observed traits. Comparison of the analyzed results obtained for the "immortalized F2" population with those for the mid-parent heterosis dataset indicated identical genetic modes of action for mid-parent heterosis and grain yield performance of the hybrid.
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Affiliation(s)
- Tingting Guo
- National Maize Improvement Center, China Agricultural University, Beijing, 100193, China
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Jain M, Moharana KC, Shankar R, Kumari R, Garg R. Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:253-64. [PMID: 24460890 DOI: 10.1111/pbi.12133] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 09/10/2013] [Accepted: 09/12/2013] [Indexed: 05/04/2023]
Abstract
Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole-genome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice.
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Affiliation(s)
- Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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Cai C, Ye W, Zhang T, Guo W. Association analysis of fiber quality traits and exploration of elite alleles in Upland cotton cultivars/accessions (Gossypium hirsutum L.). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2014; 56:51-62. [PMID: 24428209 DOI: 10.1111/jipb.12124] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 10/28/2013] [Indexed: 05/02/2023]
Abstract
Exploring the elite alleles and germplasm accessions related to fiber quality traits will accelerate the breeding of cotton for fiber quality improvement. In this study, 99 Gossypium hirsutum L. accessions with diverse origins were used to perform association analysis of fiber quality traits using 97 polymorphic microsatellite marker primer pairs. A total of 107 significant marker-trait associations were detected for three fiber quality traits under three different environments, with 70 detected in two or three environments and 37 detected in only one environment. Among the 70 significant marker-trait associations, 52.86% were reported previously, implying that these are stable loci for target traits. Furthermore, we detected a large number of elite alleles associated simultaneously with two or three traits. These elite alleles were mainly from accessions collected in China, introduced to China from the United States, or rare alleles with a frequency of less than 5%. No one cultivar contained more than half of the elite alleles, but 10 accessions were collected from China and the two introduced from the United States did contain more than half of these alleles. Therefore, there is great potential for mining elite alleles from germplasm accessions for use in fiber quality improvement in modern cotton breeding.
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Affiliation(s)
- Caiping Cai
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China
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Wang Z, Zhang D, Wang X, Tan X, Guo H, Paterson AH. A whole-genome DNA marker map for cotton based on the D-genome sequence of Gossypium raimondii L. G3 (BETHESDA, MD.) 2013; 3:1759-67. [PMID: 23979945 PMCID: PMC3789800 DOI: 10.1534/g3.113.006890] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 08/04/2013] [Indexed: 12/31/2022]
Abstract
We constructed a very-high-density, whole-genome marker map (WGMM) for cotton by using 18,597 DNA markers corresponding to 48,958 loci that were aligned to both a consensus genetic map and a reference genome sequence. The WGMM has a density of one locus per 15.6 kb, or an average of 1.3 loci per gene. The WGMM was anchored by the use of colinear markers to a detailed genetic map, providing recombinational information. Mapped markers occurred at relatively greater physical densities in distal chromosomal regions and lower physical densities in the central regions, with all 1 Mb bins having at least nine markers. Hotspots for quantitative trait loci and resistance gene analog clusters were aligned to the map and DNA markers identified for targeting of these regions of high practical importance. Based on the cotton D genome reference sequence, the locations of chromosome structural rearrangements plotted on the map facilitate its translation to other Gossypium genome types. The WGMM is a versatile genetic map for marker assisted breeding, fine mapping and cloning of genes and quantitative trait loci, developing new genetic markers and maps, genome-wide association mapping, and genome evolution studies.
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Affiliation(s)
| | | | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605
| | - Xu Tan
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605
| | - Hui Guo
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30605
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Guo X, Guo Y, Ma J, Wang F, Sun M, Gui L, Zhou J, Song X, Sun X, Zhang T. Mapping heterotic loci for yield and agronomic traits using chromosome segment introgression lines in cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:759-74. [PMID: 23570369 DOI: 10.1111/jipb.12054] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/14/2013] [Indexed: 05/12/2023]
Abstract
In the present study, a set of chromosome segment introgression lines (CSILs) using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids. Two sets of F₁ populations individually derived from CSILs crossing with both parents were configured to investigate heterotic loci (HL) and substitution effect loci (SL). A total of 58 HL and 39 SL were identified in 3 years. One stable HL, hLP-A4-3, could be detected in all 3 years. Three HLs, hBS-A8-1, hLP-D6-1, and hSI-D7-11, could be detected in 2 years. Four SLs, sBS-D7-1, sLP-A8-1, sLP-D7-1, and sLP-D12-1, could be detected in 2 years. HL and SL tended to be distributed in some HL-rich chromosome segments with close positions. Compared with QTL detected in a former study, HL showed little overlap with QTL, indicating that trait phenotype and heterosis might be controlled by different sets of loci. All three forms of genetic effects (partial-, full-, over-dominant) were identified, while the over-dominant effect made the main contribution to heterosis. These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.
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Affiliation(s)
- Xian Guo
- College of Agronomy/National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
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LIU CHUANXIANG, YUAN DAOJUN, ZHANG XIANLONG, LIN ZHONGXU. Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP. J Genet 2013. [DOI: 10.1007/s12041-013-0238-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Claverie M, Souquet M, Jean J, Forestier-Chiron N, Lepitre V, Pré M, Jacobs J, Llewellyn D, Lacape JM. cDNA-AFLP-based genetical genomics in cotton fibers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:665-683. [PMID: 22080217 DOI: 10.1007/s00122-011-1738-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2010] [Accepted: 10/18/2011] [Indexed: 05/31/2023]
Abstract
Genetical genomics, or genetic analysis applied to gene expression data, has not been widely used in plants. We used quantitative cDNA-AFLP to monitor the variation in the expression level of cotton fiber transcripts among a population of inter-specific Gossypium hirsutum × G. barbadense recombinant inbred lines (RILs). Two key fiber developmental stages, elongation (10 days post anthesis, dpa), and secondary cell wall thickening (22 dpa), were studied. Normalized intensity ratios of 3,263 and 1,201 transcript-derived fragments (TDFs) segregating over 88 RILs were analyzed for quantitative trait loci (QTL) mapping for the 10 and 22 dpa fibers, respectively. Two-thirds of all TDFs mapped between 1 and 6 eQTLs (LOD > 3.5). Chromosome 21 had a higher density of eQTLs than other chromosomes in both data sets and, within chromosomes, hotspots of presumably trans-acting eQTLs were identified. The eQTL hotspots were compared to the location of phenotypic QTLs for fiber characteristics among the RILs, and several cases of co-localization were detected. Quantitative RT-PCR for 15 sequenced TDFs showed that 3 TDFs had at least one eQTL at a similar location to those identified by cDNA-AFLP, while 3 other TDFs mapped an eQTL at a similar location but with opposite additive effect. In conclusion, cDNA-AFLP proved to be a cost-effective and highly transferable platform for genome-wide and population-wide gene expression profiling. Because TDFs are anonymous, further validation and interpretation (in silico analysis, qPCR gene profiling) of the eQTL and eQTL hotspots will be facilitated by the increasing availability of cDNA and genomic sequence resources in cotton.
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Affiliation(s)
- Michel Claverie
- UMR AGAP, CIRAD, Avenue Agropolis, 34398, Montpellier, France
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