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Zhang Q, Sun T, Wang J, Fei J, Liu Y, Liu L, Wang P. Genome-wide association study and high-quality gene mining related to soybean protein and fat. BMC Genomics 2023; 24:596. [PMID: 37805454 PMCID: PMC10559447 DOI: 10.1186/s12864-023-09687-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Soybean is one of the most important oil crops in the world, and its protein and fat are the primary sources of edible oil and vegetable protein. The effective components in soybean protein and fat have positive effects on improving human immunity, anti-tumor, and regulating blood lipids and metabolism. Therefore, increasing the contents of protein and fat in soybeans is essential for improving the quality of soybeans. RESULTS This study selected 292 soybean lines from different regions as experimental materials, based on SLAF-seq sequencing technology, and performed genome-wide association study (GWAS) on the phenotype data from 2019-2021 Planted at the experimental base of Jilin Agricultural University, such as the contents of protein and fat of soybeans. Through the GLM model and MLM model, four SNP sites (Gm09_39012959, Gm12_35492373, Gm16_9297124, and Gm20_24678362) that were significantly related to soybean fat content were associated for three consecutive years, and two SNP sites (Gm09_39012959 and Gm20_24678362) that were significantly related to soybean protein content were associated. By the annotation and enrichment of genes within the 100 Kb region of SNP loci flanking, two genes (Glyma.09G158100 and Glyma.09G158200) related to soybean protein synthesis and one gene (Glyma.12G180200) related to lipid metabolism were selected. By the preliminary verification of expression levels of genes with qPCR, it is found that during the periods of R6 and R7 of the accumulation of soybean protein and fat, Glyma.09G158100 and Glyma.09G158200 are positive regulatory genes that promote protein synthesis and accumulation, while Glyma.12G180200 is the negative regulatory gene that inhibits fat accumulation. CONCLUSIONS These results lay the basis for further verifying the gene function and studying the molecular mechanisms regulating the accumulation of protein and fat in soybean seeds.
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Affiliation(s)
- Qi Zhang
- Jilin Agricultural University, Changchun, China
| | | | - Jiabao Wang
- Jilin Agricultural University, Changchun, China
| | - JianBo Fei
- JiLin Agricultural Science and Technology University, Jilin, China
| | - Yufu Liu
- Jilin Provincial Seed Management Station, Jilin, China
| | - Lu Liu
- Jilin Agricultural University, Changchun, China
| | - Peiwu Wang
- Jilin Agricultural University, Changchun, China.
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Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2214-2256. [PMID: 36899210 DOI: 10.1007/s11427-022-2278-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/09/2023] [Indexed: 03/12/2023]
Abstract
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.
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Affiliation(s)
- Xingpeng Wen
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhiwen Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Maojun Wang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shuangxia Jin
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Zhang
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China
| | - Lingjian Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jianying Li
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Sumbul Saeed
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun Wang
- College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Zhaosheng Kong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
- Shanxi Agricultural University, Jinzhong, 030801, China.
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Xianlong Zhang
- Hubei Hongshan Laboratory, National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xiaoya Chen
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, University of CAS, Chinese Academy of Sciences, Shanghai, 200032, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
| | - Yuxian Zhu
- Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
- College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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Ma B, Zhu J, Huang X. Diversification of plant SUPPRESSOR OF MAX2 1 (SMAX1)-like genes and genome-wide identification and characterization of cotton SMXL gene family. BMC PLANT BIOLOGY 2023; 23:419. [PMID: 37691127 PMCID: PMC10494346 DOI: 10.1186/s12870-023-04421-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND Strigolactones (SLs) are a recently discovered class of plant hormones. SUPPRESSOR OF MAX2 1 (SMAX1)-like proteins, key component of the SL signaling pathway, have been studied extensively for their roles in regulating plant growth and development, such as plant branching. However, systematic identification and functional characterization of SMXL genes in cotton (Gossypium sp.), an important fiber and oil crop, has rarely been conducted. RESULTS We identified 210 SMXL genes from 21 plant genomes and examined their evolutionary relationships. The structural characteristics of the SMXL genes and their encoded proteins exhibited both consistency and diversity. All plant SMXL proteins possess a conserved Clp-N domain, P-loop NTPase, and EAR motif. We identified 63 SMXL genes in cotton and classified these into four evolutionary branches. Gene expression analysis revealed tissue-specific expression patterns of GhSMXL genes, with some upregulated in response to GR24 treatment. Protein co-expression network analysis showed that GhSMXL6, GhSMXL7-1, and GhSMXL7-2 mainly interact with proteins functioning in growth and development, while virus-induced gene silencing revealed that GhSMAX1-1 and GhSMAX1-2 suppress the growth and development of axillary buds. CONCLUSIONS SMXL gene family members show evolutionary diversification through the green plant lineage. GhSMXL6/7-1/7-2 genes play critical roles in the SL signaling pathway, while GhSMXL1-1 and GhSMXL1-2 function redundantly in growth of axillary buds. Characterization of the cotton SMXL gene family provides new insights into their roles in responding to SL signals and in plant growth and development. Genes identified in this study could be used as the candidate genes for improvement of plant architecture and crop yield.
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Affiliation(s)
- Bin Ma
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China
| | - Jianbo Zhu
- College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xianzhong Huang
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, 233100, China.
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McGarry RC, Kaur H, Lin YT, Puc GL, Eshed Williams L, van der Knaap E, Ayre BG. Altered expression of SELF-PRUNING disrupts homeostasis and facilitates signal delivery to meristems. PLANT PHYSIOLOGY 2023; 192:1517-1531. [PMID: 36852887 PMCID: PMC10231363 DOI: 10.1093/plphys/kiad126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 06/01/2023]
Abstract
Meristem maintenance, achieved through the highly conserved CLAVATA-WUSCHEL (CLV-WUS) regulatory circuit, is fundamental in balancing stem cell proliferation with cellular differentiation. Disruptions to meristem homeostasis can alter meristem size, leading to enlarged organs. Cotton (Gossypium spp.), the world's most important fiber crop, shows inherent variation in fruit size, presenting opportunities to explore the networks regulating meristem homeostasis and to impact fruit size and crop value. We identified and characterized the cotton orthologs of genes functioning in the CLV-WUS circuit. Using virus-based gene manipulation in cotton, we altered the expression of each gene to perturb meristem regulation and increase fruit size. Targeted alteration of individual components of the CLV-WUS circuit modestly fasciated flowers and fruits. Unexpectedly, controlled expression of meristem regulator SELF-PRUNING (SP) increased the impacts of altered CLV-WUS expression on flower and fruit fasciation. Meristem transcriptomics showed SP and genes of the CLV-WUS circuit are expressed independently from each other, suggesting these gene products are not acting in the same path. Virus-induced silencing of GhSP facilitated the delivery of other signals to the meristem to alter organ specification. SP has a role in cotton meristem homeostasis, and changes in GhSP expression increased access of virus-derived signals to the meristem.
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Affiliation(s)
- Róisín C McGarry
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
| | - Harmanpreet Kaur
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
| | - Yen-Tung Lin
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
| | - Guadalupe Lopez Puc
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco, Biotecnología Vegetal, subsede Sureste, 97302 Mérida, México
| | - Leor Eshed Williams
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Esther van der Knaap
- Center for Applied Genetic Technologies, College of Agricultural and Environmental Sciences, University of Georgia, Athens, GA 30602, USA
| | - Brian G Ayre
- Department of Biological Sciences and BioDiscovery Institute, University of North Texas, Denton, TX 76203-5017, USA
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Yang Z, Gao C, Zhang Y, Yan Q, Hu W, Yang L, Wang Z, Li F. Recent progression and future perspectives in cotton genomic breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:548-569. [PMID: 36226594 DOI: 10.1111/jipb.13388] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 10/11/2022] [Indexed: 05/26/2023]
Abstract
Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content. Progress in cotton genomics promotes the advancement of cotton genetics, evolutionary studies, functional genetics, and breeding, and has ushered cotton research and breeding into a new era. Here, we summarize high-impact genomics studies for cotton from the last 10 years. The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studies. We next review recent progress in cotton molecular biology and genetics, which builds on cotton genome sequencing efforts, population studies, and functional genomics, to provide insights into the mechanisms shaping abiotic and biotic stress tolerance, plant architecture, seed oil content, and fiber development. We also suggest the application of novel technologies and strategies to facilitate genome-based crop breeding. Explosive growth in the amount of novel genomic data, identified genes, gene modules, and pathways is now enabling researchers to utilize multidisciplinary genomics-enabled breeding strategies to cultivate "super cotton", synergistically improving multiple traits. These strategies must rise to meet urgent demands for a sustainable cotton industry.
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Affiliation(s)
- Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Chenxu Gao
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Yihao Zhang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Qingdi Yan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Hu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
| | - Lan Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572000, China
- Sanya Institute, Zhengzhou University, Sanya, 572000, China
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450000, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Jia X, Wang S, Zhao H, Zhu J, Li M, Wang G. QTL mapping and BSA-seq map a major QTL for the node of the first fruiting branch in cotton. FRONTIERS IN PLANT SCIENCE 2023; 14:1113059. [PMID: 36760643 PMCID: PMC9905821 DOI: 10.3389/fpls.2023.1113059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
Understanding the genetic basis of the node of the first fruiting branch (NFFB) improves early-maturity cotton breeding. Here we report QTL mapping on 200 F2 plants and derivative F2:3 and F2:4 populations by genotyping by sequencing (GBS). BC1F2 population was constructed by backcrossing one F2:4 line with the maternal parent JF914 and used for BSA-seq for further QTL mapping. A total of 1,305,642 SNPs were developed between the parents by GBS, and 2,907,790 SNPs were detected by BSA-seq. A high-density genetic map was constructed containing 11,488 SNPs and spanning 4,202.12 cM in length. A total of 13 QTL were mapped in the 3 tested populations. JF914 conferred favorable alleles for 11 QTL, and JF173 conferred favorable alleles for the other 2 QTL. Two stable QTL were repeatedly mapped in F2:3 and F2:4, including qNFFB-D3-1 and qNFFB-D6-1. Only qNFFB-D3-1 contributed more than 10% of the phenotypic variation. This QTL covered about 24.7 Mb (17,130,008-41,839,226 bp) on chromosome D3. Two regions on D3 (41,779,195-41,836,120 bp, 41,836,768-41,872,287 bp) were found by BSA-seq and covered about 92.4 Kb. This 92.4 Kb region overlapped with the stable QTL qNFFB-D3-1 and contained 8 annotated genes. By qRT-PCR, Ghir_D03G012430 showed a lower expression level from the 1- to 2-leaf stage and a higher expression level from the 3- to 6-leaf stage in the buds of JF173 than that of JF914. Ghir_D03G012390 reached the highest level at the 3- and 5-leaf stages in the buds of JF173 and JF914, respectively. As JF173 has lower NFFB and more early maturity than JF914, these two genes might be important in cell division and differentiation during NFFB formation in the seedling stage. The results of this study will facilitate a better understanding of the genetic basis of NFFB and benefit cotton molecular breeding for improving earliness traits.
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Zhou Y, Yao M, Wang Q, Zhang X, Di H, Zhang L, Dong L, Xu Q, Liu X, Zeng X, Wang Z. Analysis of QTLs and Candidate Genes for Tassel Symptoms in Maize Infected with Sporisorium reilianum. Int J Mol Sci 2022; 23:ijms232214416. [PMID: 36430897 PMCID: PMC9692487 DOI: 10.3390/ijms232214416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/13/2022] [Accepted: 11/17/2022] [Indexed: 11/22/2022] Open
Abstract
Heat smut is a fungal soil-borne disease caused by Sporisorium reilianum, and affects the development of male and female tassels. Our previous research found that the tassel symptoms in maize infected with Sporisorium reilianum significantly differed in inbred lines with Sipingtou blood, and exhibited stable heredity over time at multiple locations. In this study, cytological analysis demonstrated that the cellular organization structures of three typical inbred lines (Huangzao4, Jing7, and Chang7-2) showed significant discrepancies at the VT stage. QTLs that control the different symptoms of maize tassels infected with Sporisorium reilianum were located in two F2 populations, which were constructed using three typical inbred lines. The BSA (bulked segregation analysis) method was used to construct mixed gene pools based on typical tassel symptoms. The QTLs of different symptoms of maize tassels infected with Sporisorium reilianum were detected with 869 SSR markers covering the whole maize genome. The mixed gene pools were screened with polymorphic markers between the parents. Additional SSR markers were added near the above marker to detect genotypes in partially single plants in F2 populations. The QTL controlling tassel symptoms in the Huangzao4 and Jing7 lines was located on the bin 1.06 region, between the markers of umc1590 and bnlg1598, and explained 21.12% of the phenotypic variation with an additive effect of 0.6524. The QTL controlling the tassel symptoms of the Jing7 and Chang7-2 lines was located on the bin 2.07 region, between the markers of umc1042 and bnlg1335, and explained 11.26% phenotypic variation with an additive effect of 0.4355. Two candidate genes (ZmABP2 and Zm00001D006403) were identified by a conjoint analysis of label-free quantification proteome sequencings.
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Schilbert HM, Pucker B, Ries D, Viehöver P, Micic Z, Dreyer F, Beckmann K, Wittkop B, Weisshaar B, Holtgräwe D. Mapping‑by‑Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters in Brassica napus. Genes (Basel) 2022; 13:genes13071131. [PMID: 35885914 PMCID: PMC9317104 DOI: 10.3390/genes13071131] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
Rapeseed (Brassica napus L.) is an important oil crop and has the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction in seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping by sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals, we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant association with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus.
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Affiliation(s)
- Hanna Marie Schilbert
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Faculty of Technology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany
| | - Boas Pucker
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, Mendelssohnstraße 4, 38106 Braunschweig, Germany
| | - David Ries
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
| | - Prisca Viehöver
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
| | - Zeljko Micic
- Deutsche Saatveredelung AG, Weissenburger Straße 5, 59557 Lippstadt, Germany;
| | - Felix Dreyer
- NPZ Innovation GmbH, Hohenlieth-Hof 1, 24363 Holtsee, Germany; (F.D.); (K.B.)
| | - Katrin Beckmann
- NPZ Innovation GmbH, Hohenlieth-Hof 1, 24363 Holtsee, Germany; (F.D.); (K.B.)
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany;
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, CeBiTec & Faculty of Biology, Bielefeld University, Universitätsstraße 27, 33615 Bielefeld, Germany; (H.M.S.); (B.P.); (D.R.); (P.V.); (B.W.)
- Correspondence:
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Chao L, Pan Z, Wang J, Wu Y, Shui G, Aini N, Tang B, Guo C, Han P, Shao P, Tian X, Chang X, An Q, Ma C, You C, Zhu L, Nie X. Genetic Mapping and Analysis of a Compact Plant Architecture and Precocious Mutant in Upland Cotton. PLANTS 2022; 11:plants11111483. [PMID: 35684255 PMCID: PMC9182648 DOI: 10.3390/plants11111483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 11/16/2022]
Abstract
With the promotion and popularization of machine cotton-picking, more and more attention has been paid to the selection of early-maturity varieties with compact plant architecture. The type of fruit branch is one of the most important factors affecting plant architecture and early maturity of cotton. Heredity analysis of the cotton fruit branch is beneficial to the breeding of machine-picked cotton. Phenotype analysis showed that the types of fruit branches in cotton are controlled by a single recessive gene. Using an F2 population crossed with Huaxin102 (normal branch) and 04N-11 (nulliplex branch), BSA (Bulked Segregant Analysis) resequencing analysis and GhNB gene cloning in 04N-11, and allelic testing, showed that fruit branch type was controlled by the GhNB gene, located on chromosome D07. Ghnb5, a new recessive genotype of GhNB, was found in 04N-11. Through candidate gene association analysis, SNP 20_15811516_SNV was found to be associated with plant architecture and early maturity in the Xinjiang natural population. The GhNB gene, which is related to early maturity and the plant architecture of cotton, is a branch-type gene of cotton. The 20_15811516_SNV marker, obtained from the Xinjiang natural population, was used for the assisted breeding of machine-picked cotton varieties.
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Affiliation(s)
- Lei Chao
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Zhenyuan Pan
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Jing Wang
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China;
| | - Yuanlong Wu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, China;
| | - Guangling Shui
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Nurimanguli Aini
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Binghui Tang
- Cotton Research Institute of the Shihezi Academy of Agriculture Science, Shihezi 832011, China;
| | - Chunping Guo
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Peng Han
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Panxia Shao
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Xiaomin Tian
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Xinyi Chang
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Qiushuang An
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Chunmei Ma
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
| | - Chunyuan You
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Cotton Research Institute of the Shihezi Academy of Agriculture Science, Shihezi 832011, China;
- Correspondence: (C.Y.); (L.Z.); (X.N.)
| | - Longfu Zhu
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan 430070, China;
- Correspondence: (C.Y.); (L.Z.); (X.N.)
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Production and Construction Corps, Agricultural College, Shihezi University, Shihezi 832003, China; (L.C.); (Z.P.); (G.S.); (N.A.); (C.G.); (P.H.); (P.S.); (X.T.); (X.C.); (Q.A.); (C.M.)
- Correspondence: (C.Y.); (L.Z.); (X.N.)
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10
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Wang P, Dong N, Wang M, Sun G, Jia Y, Geng X, Liu M, Wang W, Pan Z, Yang Q, Li H, Wei C, Wang L, Zheng H, He S, Zhang X, Wang Q, Du X. Introgression from Gossypium hirsutum is a driver for population divergence and genetic diversity in Gossypium barbadense. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:764-780. [PMID: 35132720 DOI: 10.1111/tpj.15702] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/22/2022] [Accepted: 02/03/2022] [Indexed: 05/26/2023]
Affiliation(s)
- Pengpeng Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Na Dong
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, China
| | - Yinhua Jia
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Xiaoli Geng
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Weipeng Wang
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Zhaoe Pan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Qiuyue Yang
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Hongge Li
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Chunyan Wei
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Liru Wang
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | | | - Shoupu He
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Qinglian Wang
- Henan Key Laboratory of Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Collaborative Innovation Center of Modern Biological Breeding in Henan Province, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xiongming Du
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences/Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
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11
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Razzaq A, Zafar MM, Ali A, Hafeez A, Sharif F, Guan X, Deng X, Pengtao L, Shi Y, Haroon M, Gong W, Ren M, Yuan Y. The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton. Front Genet 2022; 12:642595. [PMID: 35401652 PMCID: PMC8988190 DOI: 10.3389/fgene.2021.642595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/25/2021] [Indexed: 02/02/2023] Open
Abstract
Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.
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Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Arfan Ali
- FB Genetics Four Brothers Group, Lahore, Pakistan
| | - Abdul Hafeez
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Faiza Sharif
- University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan
| | | | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Li Pengtao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Maozhi Ren
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Youlu Yuan
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
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12
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Wen T, Liu C, Wang T, Wang M, Tang F, He L. Genomic mapping and identification of candidate genes encoding nulliplex-branch trait in sea-island cotton ( Gossypium barbadense L.) by multi-omics analysis. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:34. [PMID: 37309326 PMCID: PMC10236067 DOI: 10.1007/s11032-021-01229-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/06/2021] [Indexed: 06/14/2023]
Abstract
Nulliplex branch is a key architectural trait in sea-island cotton (Gossypium barbadense L.), but its genetic basis is not well understood. Here we investigated the genetic basis of the nulliplex-branch trait in cotton by combining newly created bulked segregant analysis (BSA)-seq data, published RNA-seq data, and published whole-genome resequencing (WGR) data. We delimited the nulliplex-branch locus (qD07-NB) to D07, region 14.8-17.1 Mb, using various BSA methods and markers. We integrated our BSA data with WGR data of sea-island cotton varieties and detected a missense single-nucleotide polymorphism in the candidate gene (Gbar_D07G011870) of qD07-NB. This gene was under positive selection during sea-island cotton breeding in the Xinjiang Uygur Autonomous Region, China. Notably, the nulliplex-branch varieties possessed a better fiber quality than the long-branch varieties, and a set of high-quality molecular markers was identified for molecular breeding of the nulliplex-branch trait in cotton. We combined BSA-seq and RNA-seq data to compare gene expression profiles between two elite sea-island cotton varieties during three developmental stages. We identified eleven relevant candidate genes, five downregulated and six upregulated, in the qD07-NB locus. This research will expand our understanding of the genetic basis of the nulliplex-branch trait and provide guidance for architecture-focused breeding in cotton. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01229-w.
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Affiliation(s)
- Tianwang Wen
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Chunyan Liu
- College of Plant Science, Tarim University, Alaer, 843300 Xinjiang China
| | - Tianyou Wang
- College of Plant Science, Tarim University, Alaer, 843300 Xinjiang China
| | - Mengxing Wang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Feiyu Tang
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Liangrong He
- College of Plant Science, Tarim University, Alaer, 843300 Xinjiang China
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13
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Dong Z, Alam MK, Xie M, Yang L, Liu J, Helal MMU, Huang J, Cheng X, Liu Y, Tong C, Zhao C, Liu S. Mapping of a major QTL controlling plant height using a high-density genetic map and QTL-seq methods based on whole-genome resequencing in Brassica napus. G3-GENES GENOMES GENETICS 2021; 11:6219302. [PMID: 33836054 PMCID: PMC8495924 DOI: 10.1093/g3journal/jkab118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022]
Abstract
Plant height is a crucial element related to plant architecture that influences the seed yield of oilseed rape (Brassica napus L.). In this study, we isolated a natural B. napus mutant, namely a semi-dwarf mutant (sdw-e), which exhibits a 30% reduction in plant height compared with Zhongshuang 11-HP (ZS11-HP). Quantitative trait locus sequencing (QTL-seq) was conducted using two extreme DNA bulks in F2 populations in Wuchang-2017 derived from ZS11-HP × sdw-e to identify QTLs associated with plant height. The result suggested that two QTL intervals were located on chromosome A10. The F2 population consisting of 200 individuals in Yangluo-2018 derived from ZS11-HP × sdw-e was used to construct a high-density linkage map using whole-genome resequencing. The high-density linkage map harbored 4323 bin markers and covered a total distance of 2026.52 cM with an average marker interval of 0.47 cM. The major QTL for plant height named qPHA10 was identified on linkage group A10 by interval mapping and composite interval mapping methods. The major QTL qPHA10 was highly consistent with the QTL-seq results. And then, we integrated the variation sites and expression levels of genes in the major QTL interval to predict the candidate genes. Thus, the identified QTL and candidate genes could be used in marker-assisted selection for B. napus breeding in the future.
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Affiliation(s)
- Zhixue Dong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Muhammad Khorshed Alam
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Meili Xie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Li Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,Biosystematics Group, Experimental Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Jie Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - M M U Helal
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Junyan Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Xiaohui Cheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Yueying Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Chaobo Tong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Chuanji Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Shengyi Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
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14
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McGarry RC, Ayre BG. Cotton architecture: examining the roles of SINGLE FLOWER TRUSS and SELF-PRUNING in regulating growth habits of a woody perennial crop. CURRENT OPINION IN PLANT BIOLOGY 2021; 59:101968. [PMID: 33418402 DOI: 10.1016/j.pbi.2020.10.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 09/09/2020] [Accepted: 10/01/2020] [Indexed: 06/12/2023]
Abstract
By specifying patterns of determinate and indeterminate growth, FLOWERING LOCUS T/SINGLE FLOWER TRUSS (SFT) and TERMINAL FLOWER 1/SELF-PRUNING (SP) regulate plant architecture. Though well characterized in Arabidopsis, the impacts of these genes on the architectures of diverse crops cultivated in different environments, and their potential to enhance crop productivity and management, are less well addressed. Cotton (Gossypium spp.) is naturally a short-day photoperiodic perennial that is now grown primarily as a day-neutral, annual row crop. Different environments and cultivation practices favor specific growth habits to optimize yield, and in cotton, especially in regions that rely heavily on mechanized harvest, the trend has been to more determinate varieties. Identifying and functionally characterizing SFT and SP homologs in cotton uncovered new aspects of how ratios of indeterminate and determinate growth are balanced, and unraveling their genetic networks emphasized how broadly these gene products affect cotton growth habits.
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Affiliation(s)
- Roisin C McGarry
- BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, TX 76203-5017, USA.
| | - Brian G Ayre
- BioDiscovery Institute, Department of Biological Sciences, University of North Texas, Denton, TX 76203-5017, USA
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15
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Cheng S, Chen P, Su Z, Ma L, Hao P, Zhang J, Ma Q, Liu G, Liu J, Wang H, Wei H, Yu S. High-resolution temporal dynamic transcriptome landscape reveals a GhCAL-mediated flowering regulatory pathway in cotton (Gossypium hirsutum L.). PLANT BIOTECHNOLOGY JOURNAL 2021; 19:153-166. [PMID: 32654381 PMCID: PMC7769237 DOI: 10.1111/pbi.13449] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/24/2020] [Accepted: 05/19/2020] [Indexed: 05/04/2023]
Abstract
The transition from vegetative to reproductive growth is very important for early maturity in cotton. However, the genetic control of this highly dynamic and complex developmental process remains unclear. A high-resolution tissue- and stage-specific transcriptome profile was generated from six developmental stages using 72 samples of two early-maturing and two late-maturing cotton varieties. The results of histological analysis of paraffin sections showed that flower bud differentiation occurred at the third true leaf stage (3TLS) in early-maturing varieties, but at the fifth true leaf stage (5TLS) in late-maturing varieties. Using pairwise comparison and weighted gene co-expression network analysis, 5312 differentially expressed genes were obtained, which were divided into 10 gene co-expression modules. In the MElightcyan module, 46 candidate genes regulating cotton flower bud differentiation were identified and expressed at the flower bud differentiation stage. A novel key regulatory gene related to flower bud differentiation, GhCAL, was identified in the MElightcyan module. Anti-GhCAL transgenic cotton plants exhibited late flower bud differentiation and flowering time. GhCAL formed heterodimers with GhAP1-A04/GhAGL6-D09 and regulated the expression of GhAP1-A04 and GhAGL6-D09. GhAP1-A04- and GhAGL6-D09-silenced plants also showed significant late flowering. Finally, we propose a new flowering regulatory pathway mediated by GhCAL. This study elucidated the molecular mechanism of cotton flowering regulation and provides good genetic resources for cotton early-maturing breeding.
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Affiliation(s)
- Shuaishuai Cheng
- College of AgronomyNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Pengyun Chen
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Zhengzheng Su
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Liang Ma
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Pengbo Hao
- College of AgronomyNorthwest A&F UniversityYanglingChina
| | - Jingjing Zhang
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Qiang Ma
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Guoyuan Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Ji Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Hantao Wang
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Hengling Wei
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
| | - Shuxun Yu
- College of AgronomyNorthwest A&F UniversityYanglingChina
- State Key Laboratory of Cotton BiologyKey Laboratory of Cotton Genetic ImprovementCotton Institute of the Chinese Academy of Agricultural SciencesMinistry of AgricultureAnyangChina
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16
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Cui Y, Ge Q, Zhao P, Chen W, Sang X, Zhao Y, Chen Q, Wang H. Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis. FRONTIERS IN PLANT SCIENCE 2021; 12:703011. [PMID: 34691091 PMCID: PMC8531640 DOI: 10.3389/fpls.2021.703011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/24/2021] [Indexed: 05/05/2023]
Abstract
Cotton is a globally important cash crop. Verticillium wilt (VW) is commonly known as "cancer" of cotton and causes serious loss of yield and fiber quality in cotton production around the world. Here, we performed a BSA-seq analysis using an F2:3 segregation population to identify the candidate loci involved in VW resistance. Two QTLs (qvw-D05-1 and qvw-D05-2) related to VW resistance in cotton were identified using two resistant/susceptible bulks from the F2 segregation population constructed by crossing the resistant cultivar ZZM2 with the susceptible cultivar J11. A total of 30stop-lost SNPs and 42 stop-gained SNPs, which included 17 genes, were screened in the qvw-D05-2 region by SnpEff analysis. Further analysis of the transcriptome data and qRT-PCR revealed that the expression level of Ghir_D05G037630 (designated as GhDRP) varied significantly at certain time points after infection with V. dahliae. The virus-induced gene silencing of GhDRP resulted in higher susceptibility of the plants to V. dahliae than the control, suggesting that GhDRP is involved in the resistance to V. dahlia infection. This study provides a method for rapid mining of quantitative trait loci and screening of candidate genes, as well as enriches the genomic information and gene resources for the molecular breeding of disease resistance in cotton.
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Affiliation(s)
- Yanli Cui
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Pei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaohui Sang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yunlei Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Yunlei Zhao,
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education, Xinjiang Agricultural University, Ürümqi, China
- Quanjia Chen,
| | - Hongmei Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Hongmei Wang,
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17
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Chen W, Li Y, Zhu S, Fang S, Zhao L, Guo Y, Wang J, Yuan L, Lu Y, Liu F, Yao J, Zhang Y. A Retrotransposon Insertion in GhMML3_D12 Is Likely Responsible for the Lintless Locus li3 of Tetraploid Cotton. FRONTIERS IN PLANT SCIENCE 2020; 11:593679. [PMID: 33324436 PMCID: PMC7725795 DOI: 10.3389/fpls.2020.593679] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/09/2020] [Indexed: 05/31/2023]
Abstract
Cotton (Gossypium) seed fibers can be divided into lint (long) or fuzz (very short). Using fiberless (fuzzless-lintless) mutants, the lint initiation gene Li3 was identified by map-based cloning. The gene is an R2R3-MYB transcription factor located on chromosome D12 (GhMML3_D12). Sequence analysis revealed that li3 is a loss-of-function allele containing a retrotransposon insertion in the second exon that completely blocks the gene’s expression. The genetic loci n2 and n3 underlying the recessive fuzzless phenotype in Gossypium hirsutum were also mapped. The genomic location of n3 overlapped with that of the dominant fuzzless locus N1, and n3 appeared to be a loss-of-function allele caused by a single nucleotide polymorphism (SNP) mutation in the coding region of GhMML3_A12. The n2 allele was found to be co-located with li3 and originated from G. babardense. n2 and li3 are possibly the multiple alleles of the GhMML3_D12 gene. Genetic analysis showed that Li3 and N3 are a pair of homologs with additive effects for the initiation of fibers (fuzz or lint). In addition, the presence of another locus was speculated, and it appeared to show an inhibitory effect on the expression of GhMML3. These findings provide new information about the genetic factors affecting the initiation of fibers in cotton.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shouhong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shengtao Fang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yan Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Junyi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Li Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youjun Lu
- School of Biological Science and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
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18
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Li M, Liu Y, Tao Y, Xu C, Li X, Zhang X, Han Y, Yang X, Sun J, Li W, Li D, Zhao X, Zhao L. Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study. BMC Genomics 2019; 20:987. [PMID: 31842754 PMCID: PMC6916438 DOI: 10.1186/s12864-019-6324-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 11/22/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND As a photoperiod-sensitive and self-pollinated species, the growth periods traits play important roles in the adaptability and yield of soybean. To examine the genetic architecture of soybean growth periods, we performed a genome-wide association study (GWAS) using a panel of 278 soybean accessions and 34,710 single nucleotide polymorphisms (SNPs) with minor allele frequencies (MAF) higher than 0.04 detected by the specific-locus amplified fragment sequencing (SLAF-seq) with a 6.14-fold average sequencing depth. GWAS was conducted by a compressed mixed linear model (CMLM) involving in both relative kinship and population structure. RESULTS GWAS revealed that 37 significant SNP peaks associated with soybean flowering time or other growth periods related traits including full bloom, beginning pod, full pod, beginning seed, and full seed in two or more environments at -log10(P) > 3.75 or -log10(P) > 4.44 were distributed on 14 chromosomes, including chromosome 1, 2, 3, 5, 6, 9, 11, 12, 13, 14, 15, 17, 18, 19. Fourteen SNPs were novel loci and 23 SNPs were located within known QTLs or 75 kb near the known SNPs. Five candidate genes (Glyma.05G101800, Glyma.11G140100, Glyma.11G142900, Glyma.19G099700, Glyma.19G100900) in a 90 kb genomic region of each side of four significant SNPs (Gm5_27111367, Gm11_10629613, Gm11_10950924, Gm19_34768458) based on the average LD decay were homologs of Arabidopsis flowering time genes of AT5G48385.1, AT3G46510.1, AT5G59780.3, AT1G28050.1, and AT3G26790.1. These genes encoding FRI (FRIGIDA), PUB13 (plant U-box 13), MYB59, CONSTANS, and FUS3 proteins respectively might play important roles in controlling soybean growth periods. CONCLUSIONS This study identified putative SNP markers associated with soybean growth period traits, which could be used for the marker-assisted selection of soybean growth period traits. Furthermore, the possible candidate genes involved in the control of soybean flowering time were predicted.
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Affiliation(s)
- Minmin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Ying Liu
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Yahan Tao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Chongjing Xu
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xiaoming Zhang
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xue Yang
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Jingzhe Sun
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Wenbin Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Dongmei Li
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
| | - Lin Zhao
- Key Laboratory of Soybean Biology of Ministry of Education, China (Key Laboratory of Biology and Genetics & Breeding for Soybean in Northeast China), Northeast Agricultural University, Harbin, China
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Mao G, Wei H, Hu W, Ma Q, Zhang M, Wang H, Yu S. Fine mapping and molecular characterization of the virescent gene vsp in Upland cotton (Gossypium hirsutum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:2069-2086. [PMID: 30953093 DOI: 10.1007/s00122-019-03338-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 03/26/2019] [Indexed: 05/24/2023]
Abstract
The vsp gene was fine mapped to a 353.7-kb region, and a 201-bp deletion that affected chloroplast development and chlorophyll biosynthesis was found in the candidate gene GhPUR4. Virescent mutations can be used as marker traits in heterosis breeding and can also be used to research chloroplast development, chlorophyll biosynthesis and photosynthesis mechanisms. Here, we obtained a light-sensitive virescent mutant, vsp, that has reduced chlorophyll (Chl) content and abnormal chloroplast development. Then, the virescent space (vsp) gene in the vsp mutant was preliminarily mapped to a 38.32-Mb region of chromosome D04 using a high-density SNP genetic map with a total length of 5384.33 cM and 4472 bin markers. Furthermore, the vsp gene was narrowed down to a 353.7-kb region that contains 15 candidate genes using 484 virescent individuals from an F2 population. Sequence analysis of genes in this region showed that a 201-bp deletion was present in the Gh_D04G1108 (GhPUR4) gene in the vsp mutant. The 201-bp deletion of Gh_D04G1108 caused the deletion of 67 AAs in the GhPUR4 protein. Virus-induced gene silencing (VIGS) of GhPUR4 in normal plants caused reduced GhPUR4 gene expression levels, reduced Chl content, abnormal chloroplast development and virescent true leaves. This study could help us unravel the function of GhPUR4 in chloroplast development and Chl biosynthesis at the early developmental stages of the true leaves in cotton, which could promote the research and application of virescent mutations in cotton heterosis breeding.
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Affiliation(s)
- Guangzhi Mao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, Henan, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Wei Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Qiang Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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20
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Identification of genomic regions associated with multi-silique trait in Brassica napus. BMC Genomics 2019; 20:304. [PMID: 31014236 PMCID: PMC6480887 DOI: 10.1186/s12864-019-5675-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2018] [Accepted: 04/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although rapeseed (Brassica napus L.) mutant forming multiple siliques was morphologically described and considered to increase the silique number per plant, an important agronomic trait in this crop, the molecular mechanism underlying this beneficial trait remains unclear. Here, we combined bulked-segregant analysis (BSA) and whole genome re-sequencing (WGR) to map the genomic regions responsible for the multi-silique trait using two pools of DNA from the near-isogenic lines (NILs) zws-ms (multi-silique) and zws-217 (single-silique). We used the Euclidean Distance (ED) to identify genomic regions associated with this trait based on both SNPs and InDels. We also conducted transcriptome sequencing to identify differentially expressed genes (DEGs) between zws-ms and zws-217. RESULTS Genetic analysis using the ED algorithm identified three SNP- and two InDel-associated regions for the multi-silique trait. Two highly overlapped parts of the SNP- and InDel-associated regions were identified as important intersecting regions, which are located on chromosomes A09 and C08, respectively, including 2044 genes in 10.20-MB length totally. Transcriptome sequencing revealed 129 DEGs between zws-ms and zws-217 in buds, including 39 DEGs located in the two abovementioned associated regions. We identified candidate genes involved in multi-silique formation in rapeseed based on the results of functional annotation. CONCLUSIONS This study identified the genomic regions and candidate genes related to the multi-silique trait in rapeseed.
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21
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Schrager-Lavelle A, Gath NN, Devisetty UK, Carrera E, López-Díaz I, Blázquez MA, Maloof JN. The role of a class III gibberellin 2-oxidase in tomato internode elongation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:603-615. [PMID: 30394600 DOI: 10.1111/tpj.14145] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 10/20/2018] [Accepted: 10/25/2018] [Indexed: 05/27/2023]
Abstract
A network of environmental inputs and internal signaling controls plant growth, development and organ elongation. In particular, the growth-promoting hormone gibberellin (GA) has been shown to play a significant role in organ elongation. The use of tomato as a model organism to study elongation presents an opportunity to study the genetic control of internode-specific elongation in a eudicot species with a sympodial growth habit and substantial internodes that can and do respond to external stimuli. To investigate internode elongation, a mutant with an elongated hypocotyl and internodes but wild-type petioles was identified through a forward genetic screen. In addition to stem-specific elongation, this mutant, named tomato internode elongated -1 (tie-1) is more sensitive to the GA biosynthetic inhibitor paclobutrazol and has altered levels of intermediate and bioactive GAs compared with wild-type plants. The mutation responsible for the internode elongation phenotype was mapped to GA2oxidase 7, a class III GA 2-oxidase in the GA biosynthetic pathway, through a bulked segregant analysis and bioinformatic pipeline, and confirmed by transgenic complementation. Furthermore, bacterially expressed recombinant TIE protein was shown to have bona fide GA 2-oxidase activity. These results define a critical role for this gene in internode elongation and are significant because they further the understanding of the role of GA biosynthetic genes in organ-specific elongation.
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Affiliation(s)
- Amanda Schrager-Lavelle
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Natalie N Gath
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Upendra K Devisetty
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
| | - Esther Carrera
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022, Valencia, Spain
| | - Isabel López-Díaz
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022, Valencia, Spain
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politécnica de Valencia), 46022, Valencia, Spain
| | - Julin N Maloof
- Department of Plant Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616, USA
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22
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Lu Y, Chen W, Zhao L, Yao J, Li Y, Yang W, Liu Z, Zhang Y, Sun J. Different divergence events for three pairs of PEBPs in Gossypium as implied by evolutionary analysis. Genes Genomics 2019; 41:445-458. [PMID: 30610620 DOI: 10.1007/s13258-018-0775-0] [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: 10/12/2018] [Accepted: 12/06/2018] [Indexed: 11/26/2022]
Abstract
INTRODUCTION The phosphatidylethanolamine-binding protein (PEBP) gene family plays a crucial role in seed germination, reproductive transformation, and other important developmental processes in plants, but its distribution in Gossypium genomes or species, evolutionary properties, and the fates of multiple duplicated genes remain unclear. OBJECTIVES The primary objectives of this study were to elucidate the distribution and characteristics of PEBP genes in Gossypium, as well as the evolutionary pattern of duplication and deletion, and functional differentiation of PEBPs in plants. METHODS Using the PEBP protein sequences in Arabidopsis thaliana as queries, blast alignment was carried out for the identification of PEBP genes in four sequenced cotton species. Using the primers designed according to the PEBP genome sequences, PEBP genes were cloned from 15 representative genomes of Gossypium genus, and the gene structure, CDS sequence, protein sequence and properties were predicted and phylogenetic analysis was performed. Taking PEBP proteins of grape as reference, grouping of orthologous gene, analysis of phylogeny and divergence of PEBPs in nine species were conducted to reconstruct the evolutionary pattern of PEBP genes in plants. RESULTS We identified and cloned 160 PEBPs from 15 cotton species, and the phylogenetic analysis showed that the genes could be classified into the following three subfamilies: MFT-like, FT-like and TFL1-like. There were eight single orthologous group (OG) members in each diploid and 16 double OG members in each tetraploid. An analysis of the expression and selective pressure indicated that expression divergence and strong purification selection within the same OG presented in the PEBP gene family. CONCLUSION An evolutionary pattern of duplication and deletion of the PEBP family in the evolutionary history of Gossypium was suggested, and three pairs of genes resulted from different whole-genome duplication events.
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Affiliation(s)
- Youjun Lu
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832003, China
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Huanghe Road, Anyang, 455000, Henan, China
| | - Wei Chen
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Lanjie Zhao
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Jinbo Yao
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Yan Li
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China
| | - Weijun Yang
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Huanghe Road, Anyang, 455000, Henan, China
| | - Ziyang Liu
- University of Saskatchewan, Saskatoon, SK, S7N 5A5, Canada
| | - Yongshan Zhang
- Cotton Research Institute of the Chinese Academy of Agricultural Sciences (CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, China.
| | - Jie Sun
- College of Agriculture/The Key Laboratory of Oasis Eco-Agriculture, Shihezi University, Shihezi, 832003, China.
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23
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Tang W, Huang L, Bu S, Zhang X, Wu W. Estimation of QTL heritability based on pooled sequencing data. Bioinformatics 2019; 34:978-984. [PMID: 29106443 DOI: 10.1093/bioinformatics/btx703] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/01/2017] [Indexed: 12/13/2022] Open
Abstract
Motivation Bulked segregant analysis combined with next generation sequencing has proven to be a simple and efficient approach for fast mapping of quantitative trait loci (QTLs). However, how to estimate the proportion of phenotypic variance explained by a QTL (or termed QTL heritability) in such pooled QTL mapping is an unsolved problem. Results In this paper, we propose a method called PQHE to estimate QTL heritability using pooled sequencing data obtained under different experimental designs. Simulation studies indicated that our method is correct and feasible. Four practical examples from rice and yeast are demonstrated, each representing a different situation. Availability and implementation The R scripts of our method are open source under GPLv3 license at http://genetics.fafu.edu.cn/PQHE or https://github.com/biotangweiqi/PQHE. The R scripts require the R package rootSolve. Contact wuwr@fafu.edu.cn. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Weiqi Tang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Likun Huang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Suhong Bu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Xuzhang Zhang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Life Sciences.,Fujian Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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24
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Diao Y, Zhan J, Zhao Y, Liu L, Liu P, Wei X, Ding Y, Sajjad M, Hu W, Wang P, Ge X. GhTIE1 Regulates Branching Through Modulating the Transcriptional Activity of TCPs in Cotton and Arabidopsis. FRONTIERS IN PLANT SCIENCE 2019; 10:1348. [PMID: 31719830 PMCID: PMC6827420 DOI: 10.3389/fpls.2019.01348] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 09/27/2019] [Indexed: 05/22/2023]
Abstract
Transcription factors (TFs) and transcriptional regulators are important switches in transcriptional networks. In recent years, the transcriptional regulator TIE1 (TCP interactor containing EAR motif protein 1) was identified as a nuclear transcriptional repressor which regulates leaf development and controls branch development. However, the function and regulatory network of GhTIE1 has not been studied in cotton. Here, we demonstrated that GhTIE1 is functionally conserved in controlling shoot branching in cotton and Arabidopsis. Overexpression of GhTIE1 in Arabidopsis leads to higher bud vigor and more branches, while silencing GhTIE1 in cotton reduced bud activity and increased branching inhibition. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that GhTIE1 directly interacted with subclass II TCPs (GhBRC1, GhBRC2, and GhTCP13) in vivo and in vitro. Overexpression of GhBRC1, GhBRC2, and GhTCP13 in mutant brc1-2 partially rescued the mutant phenotype and decreased the number of branches, showing that these TCPs are functionally redundant in controlling branching. A transient dual-luciferase reporter assay indicated that GhTIE1 repressed the protein activity of GhBRC1 and GhTCP13, and thereby decreased the expression of their target gene GhHB21. Gene expression level analysis in GhTIE1-overexpressed and silenced plants also proved that GhTIE1 regulated shoot branching via repressing the activity of BRC1, HB21, HB40, and HB53. Our data reveals that shoot branching can be controlled via modulation of the activity of the TIE1 and TCP proteins and provides a theoretical basis for cultivating cotton varieties with ideal plant types.
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Affiliation(s)
- Yangyang Diao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jingjing Zhan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yanyan Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Lisen Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Peipei Liu
- State Key Laboratory of Cotton Biology (Hebei Base), College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xi Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yanpeng Ding
- State Key Laboratory of Cotton Biology (Hebei Base), College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Muhammad Sajjad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Wei Hu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Peng Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- *Correspondence: Xiaoyang Ge,
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25
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Chen W, Yao J, Li Y, Zhao L, Liu J, Guo Y, Wang J, Yuan L, Liu Z, Lu Y, Zhang Y. Nulliplex-branch, a TERMINAL FLOWER 1 ortholog, controls plant growth habit in cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:97-112. [PMID: 30288552 DOI: 10.1007/s00122-018-3197-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 09/25/2018] [Indexed: 06/08/2023]
Abstract
Nulliplex-branch (nb) mutants in cotton display a specific architecture. The gene responsible for the nb phenotype was identified, and its modulation mode was further studied. Plant architecture is an important agronomic factor influencing various traits such as yield and variety adaptability in crop plants. Cotton (Gossypium) simultaneously displays monopodial and sympodial growth. Nulliplex-branch (nb) mutants showing determinate sympodial shoots have been reported in both G. hirsutum (Ghnb) and G. barbadense (Gbnb). In this study, the gene responsible for the nb phenotype was identified. GhNB and GbNB were found to be allelic loci and are TERMINAL FLOWER 1 orthologs on the Dt subgenome, though the At copies remain native. Sequencing and association analyses identified four (Gh-nb1-Gh-nb4) and one (Gb-nb1) type of point mutation in the coding sequences of Ghnb and Gbnb, respectively. The NB gene was mainly expressed in the root and shoot apex, and expression rhythms were also observed in these tissues, suggesting that the expression of the NB gene could be regulated by photoperiod. Constitutive overexpression of GhNB suppresses the differentiation of the reproductive shoots. Knockout of both copies of GhNB caused the main and lateral shoots to terminate in flowers, which is a more determinate architecture than that of the nb mutants and implies that its function might be dosage dependent. A protein lipid overlay assay indicated that the amino acid substitutions in Gh-nb1 and Gb-nb1 weaken the ligand-binding activity of the NB protein in vitro. These findings suggest that the NB gene plays crucial roles in regulating the determinacy of shoots, and the modulation of this gene should constitute an effective crop improvement approach through adjusting the growth habit of cotton.
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Affiliation(s)
- Wei Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jinbo Yao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yan Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Lanjie Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Jie Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yan Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Junyi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Li Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ziyang Liu
- Art and Science College, University of Saskatchewan, Saskatoon, S7N 5A5, Canada
| | - Youjun Lu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yongshan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
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26
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Liu D, Teng Z, Kong J, Liu X, Wang W, Zhang X, Zhai T, Deng X, Wang J, Zeng J, Xiao Y, Guo K, Zhang J, Liu D, Wang W, Zhang Z. Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton. BMC PLANT BIOLOGY 2018; 18:286. [PMID: 30458710 PMCID: PMC6245773 DOI: 10.1186/s12870-018-1518-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 11/07/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Plant architecture and the vegetative-reproductive transition have major impacts on the agronomic success of crop plants, but genetic mechanisms underlying these traits in cotton (Gossypium spp.) have not been identified. RESULTS We identify four natural mutations in GoCEN-Dt associated with cluster fruiting (cl) and early maturity. The situ hybridization shows that GhCEN is preferentially expressed in cotton shoot apical meristems (SAM) of the main stem and axillary buds. Constitutive GhCEN-Dt overexpression suppresses the transition of the cotton vegetative apex to a reproductive shoot. Silencing GoCEN leads to early flowering and determinate growth, and in tetraploids causes the main stem to terminate in a floral bud, a novel phenotype that exemplifies co-adaptation of polyploid subgenomes and suggests new research and/or crop improvement approaches. Natural cl variations are enriched in cottons adapted to high latitudes with short frost-free periods, indicating that mutants of GoCEN have been strongly selected for early maturity. CONCLUSION We show that the cotton gene GoCEN-Dt, a homolog of Antirrhinum CENTRORADIALIS, is responsible for determinate growth habit and cluster fruiting. Insight into the genetic control of branch and flower differentiation offers new approaches to develop early maturing cultivars of cotton and other crops with plant architecture appropriate for mechanical harvesting.
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Affiliation(s)
- Dexin Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Zhonghua Teng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jie Kong
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, urumqi, Xinjiang 830091 People’s Republic of China
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193 People’s Republic of China
| | - Xueying Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Wenwen Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Xiao Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Tengfei Zhai
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Xianping Deng
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jinxia Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jianyan Zeng
- Biotechnology Research Center, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Yuehua Xiao
- Biotechnology Research Center, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Kai Guo
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Dajun Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
| | - Weiran Wang
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, urumqi, Xinjiang 830091 People’s Republic of China
| | - Zhengsheng Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716 People’s Republic of China
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27
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Wang G, Chen B, Du H, Zhang F, Zhang H, Wang Y, He H, Geng S, Zhang X. Genetic mapping of anthocyanin accumulation-related genes in pepper fruits using a combination of SLAF-seq and BSA. PLoS One 2018; 13:e0204690. [PMID: 30261055 PMCID: PMC6160195 DOI: 10.1371/journal.pone.0204690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
Anthocyanins have significant functions in stress tolerance in pepper (Capsicum annuum L.) and also benefit human health. Nevertheless, the key structural genes and regulatory genes involved in anthocyanin accumulation in pepper fruits are still not well understood and fine mapped. For the present study, 383 F2 plants from a cross between the green-fruited C. annuum line Z5 and the purple-fruited line Z6 was developed. Two separate bulked DNA pools were constructed with DNAs extracted from either 37 plants with high anthocyanin content or from 18 plants with no anthocyanin. A combination of specific-locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was used to identify candidates for regions associated with anthocyanin accumulation. We identified a total of 127,004 high-quality single nucleotide polymorphism (SNP) markers, and detected 1674 high-quality SNP markers associated with anthocyanin accumulation. Three candidate anthocyanin-associated regions including the intervals from 12.48 to 20.00 Mb, from 54.67 to 56.59 Mb, and from 192.17 to 196.82 Mb were identified within a 14.10-Mb interval on chromosome 10 containing 126 candidate genes. Based on their annotations, we identified 12 candidate genes that are predicted to be associated with anthocyanin expression. The present results provide an efficient strategy for genetic mapping of and valuable insights into the genetic mechanisms of anthocyanin accumulation in pepper fruit, and allow us to clone and functionally analyze the genes that influence anthocyanin accumulation in this species.
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Affiliation(s)
- Guoyun Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Haiying Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Hongju He
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
| | - Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
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28
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Sun Q, Qiao J, Zhang S, He S, Shi Y, Yuan Y, Zhang X, Cai Y. Changes in DNA methylation assessed by genomic bisulfite sequencing suggest a role for DNA methylation in cotton fruiting branch development. PeerJ 2018; 6:e4945. [PMID: 29915693 PMCID: PMC6004305 DOI: 10.7717/peerj.4945] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 05/18/2018] [Indexed: 12/20/2022] Open
Abstract
Cotton plant architecture, including fruit branch formation and flowering pattern, influences plant light exploitation, cotton yield and planting cost. DNA methylation has been widely observed at different developmental stages in both plants and animals and is associated with regulation of gene expression, chromatin remodelling, genome protection and other functions. Here, we investigated the global epigenetic reprogramming during the development of fruiting branches and floral buds at three developmental stages: the seedling stage, the pre-squaring stage and the squaring stage. We first identified 22 cotton genes which potentially encode DNA methyltransferases and demethylases. Among them, the homologous genes of CMT, DRM2 and MET1 were upregulated at pre-squaring and squaring stages, suggesting that DNA methylation is involved in the development of floral buds and fruit branches. Although the global methylation at all of three developmental stages was not changed, the CHG-type methylation of non-expressed genes was higher than those of expressed genes. In addition, we found that the expression of the homologous genes of the key circadian rhythm regulators, including CRY, LHY and CO, was associated with changes of DNA methylation at three developmental stages.
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Affiliation(s)
- Quan Sun
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Chongqing University of Posts and Telecommunications, College of Bioinformation, ChongQing, China
| | - Jing Qiao
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Sai Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Shibin He
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
| | - Yuzhen Shi
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Youlu Yuan
- Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiao Zhang
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China.,Cotton Institute, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Yingfan Cai
- Henan University, State Key Laboratory of Cotton Biology, Henan Key Laboratory of Plant Stress Biology, School of Life Sciences, School of Computer and Information Engineering, Kaifeng, Henan, China
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29
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Su J, Li L, Zhang C, Wang C, Gu L, Wang H, Wei H, Liu Q, Huang L, Yu S. Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1299-1314. [PMID: 29497767 DOI: 10.1007/s00122-018-3079-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/24/2018] [Indexed: 05/04/2023]
Abstract
Thirty significant associations between 22 SNPs and five plant architecture component traits in Chinese upland cotton were identified via GWAS. Four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits. A candidate gene, Gh_D03G0922, might be responsible for plant height in upland cotton. A compact plant architecture is increasingly required for mechanized harvesting processes in China. Therefore, cotton plant architecture is an important trait, and its components, such as plant height, fruit branch length and fruit branch angle, affect the suitability of a cultivar for mechanized harvesting. To determine the genetic basis of cotton plant architecture, a genome-wide association study (GWAS) was performed using a panel composed of 355 accessions and 93,250 single nucleotide polymorphisms (SNPs) identified using the specific-locus amplified fragment sequencing method. Thirty significant associations between 22 SNPs and five plant architecture component traits were identified via GWAS. Most importantly, four peak SNP loci located on chromosome D03 were simultaneously associated with more plant architecture component traits, and these SNPs were harbored in one linkage disequilibrium block. Furthermore, 21 candidate genes for plant architecture were predicted in a 0.95-Mb region including the four peak SNPs. One of these genes (Gh_D03G0922) was near the significant SNP D03_31584163 (8.40 kb), and its Arabidopsis homologs contain MADS-box domains that might be involved in plant growth and development. qRT-PCR showed that the expression of Gh_D03G0922 was upregulated in the apical buds and young leaves of the short and compact cotton varieties, and virus-induced gene silencing (VIGS) proved that the silenced plants exhibited increased PH. These results indicate that Gh_D03G0922 is likely the candidate gene for PH in cotton. The genetic variations and candidate genes identified in this study lay a foundation for cultivating moderately short and compact varieties in future Chinese cotton-breeding programs.
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Affiliation(s)
- Junji Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science/Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding, Ministry of Agriculture, Shihezi, China
| | - Libei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Chi Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Caixiang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Qibao Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China
| | - Long Huang
- Shanghai Majorbio Bio-pharm Biotechnology Co. Ltd., Shanghai, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAAS, Anyang, China.
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30
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Si Z, Liu H, Zhu J, Chen J, Wang Q, Fang L, Gao F, Tian Y, Chen Y, Chang L, Liu B, Han Z, Zhou B, Hu Y, Huang X, Zhang T. Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:2543-2553. [PMID: 29547987 PMCID: PMC5920339 DOI: 10.1093/jxb/ery093] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 03/12/2018] [Indexed: 05/19/2023]
Abstract
In cotton, the formation of fruiting branches affects both plant architecture and fiber yield. Here, we report map-based cloning of the axillary flowering mutation gene (GbAF) that causes bolls to be borne directly on the main plant stem in Gossypium barbadense, and of the clustered boll mutation gene (cl1) in G. hirsutum. Both mutant alleles were found to represent point mutations at the Cl1 locus. Therefore, we propose that the GbAF mutation be referred to as cl1b. These Cl1 loci correspond to homologs of tomato SELF-PRUNING (SP), i.e. Gossypium spp. SP (GoSP) genes. In tetraploid cottons, single monogenic mutation of either duplicate GoSP gene (one in the A and one in the D subgenome) is associated with the axillary cluster flowering phenotype, although the shoot-indeterminate state of the inflorescence is maintained. By contrast, silencing of both GoSPs leads to the termination of flowering or determinate plants. The architecture of axillary flowering cotton allows higher planting density, contributing to increased fiber yield. Taken together the results provide new insights into the underlying mechanism of branching in cotton species, and characterization of GoSP genes may promote the development of compact cultivars to increase global cotton production.
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Affiliation(s)
- Zhanfeng Si
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hui Liu
- Special Plant Genomics Laboratory, College of Life Sciences, University of Shihezi, Shihezi, Xinjiang, China
| | - Jiankun Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Jiedan Chen
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qiong Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Lei Fang
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Fengkai Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yue Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yali Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Lijing Chang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Bingliang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Zegang Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Yan Hu
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Xianzhong Huang
- Special Plant Genomics Laboratory, College of Life Sciences, University of Shihezi, Shihezi, Xinjiang, China
- Correspondence: or
| | - Tianzhen Zhang
- Agronomy Department, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Hybrid R & D Engineering Center (the Ministry of Education), College of Agriculture, Nanjing Agricultural University, Nanjing, China
- Correspondence: or
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31
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Zhang X, Wang G, Chen B, Du H, Zhang F, Zhang H, Wang Q, Geng S. Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA. PLoS One 2018; 13:e0194071. [PMID: 29558466 PMCID: PMC5860747 DOI: 10.1371/journal.pone.0194071] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/23/2018] [Indexed: 02/05/2023] Open
Abstract
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.), but the genetic mechanisms that control FFN are still poorly understood. In the present study, we developed 249 F2 plants derived from an intraspecific cross between the inbred pepper lines Z4 and Z5. Thirty plants with the highest FFN and 30 plants with the lowest FFN were chosen and their DNAs were pooled according to phenotype to construct two bulked DNA pools. Specific-locus amplified fragment sequencing (SLAF-seq) was combined with bulked segregant analysis (BSA) to identify candidate regions related to FFN. According to our genetic analysis, the FFN trait is quantitatively inherited. A total of 106,848 high-quality single nucleotide polymorphism (SNP) markers were obtained, and 393 high-quality SNP markers associated with FFN were detected. Ten candidate regions within an interval of 3.98 Mb on chromosome 12 harboring 23 candidate genes were identified as closely correlated with FFN. Five genes (CA12g15130, CA12g15160, CA12g15370, CA12g15360, and CA12g15390) are predicted based on their annotations to be associated with expression of the FFN trait. The present study demonstrates an efficient genetic mapping strategy and lays a good foundation for molecular marker-assisted breeding using SNP markers linked to FFN and for cloning and functional analysis of the key genes controlling FFN.
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Affiliation(s)
- Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- College of Horticulture, China Agricultural University, Beijing, P.R. China
| | - Guoyun Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Haiying Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Qian Wang
- College of Horticulture, China Agricultural University, Beijing, P.R. China
- * E-mail: (SG); (QW)
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (QW)
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32
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Zhu QH, Yuan Y, Stiller W, Jia Y, Wang P, Pan Z, Du X, Llewellyn D, Wilson I. Genetic dissection of the fuzzless seed trait in Gossypium barbadense. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:997-1009. [PMID: 29351643 PMCID: PMC6018843 DOI: 10.1093/jxb/erx459] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 11/29/2017] [Indexed: 05/21/2023]
Abstract
Cotton fibres are single-celled trichomes arising from the epidermal cells of the seed coat and may be either long (lint) or very short (fuzz). The dominant fuzzless N1 of Gossypium hirsutum is a defective allele of the At-subgenome homoeolog of MYB25-like, but the genetic components underlying the recessive fuzzless trait from G. barbadense (Gb) are unknown. We have identified five genetic loci, including a major contributing locus containing MYB25-like_Dt, associated with Gb fuzzless seeds based on genotyping of fuzzy and fuzzless near isogenic lines (NILs) from an interspecies cross (G. barbadense × G. hirsutum). At 3 d post-anthesis when fuzz fibres are initiating, expression of MYB25-like_Dt was significantly lower in fuzzless NILs than in fuzzy seeded NILs, while higher MYB25-like_Dt expression was associated with more seed fuzz across different cotton genotypes. Phenotypic and genotypic analysis of MYB25-like homoeoalleles in cottons showing different fibre phenotypes and their crossing progeny indicated that both MYB25-like_At and MYB25-like_Dt are associated with lint development, and that fuzz development is mainly determined by the expression level of MYB25-like_Dt at ~3 d post-anthesis. Expression of Gb fuzzless seeds depends on genetic background and interactions amongst the multiple loci identified. MYB25-like_Dt is one of the best candidates for N2.
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Affiliation(s)
- Qian-Hao Zhu
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Correspondence: and
| | - Yuman Yuan
- CSIRO Agriculture and Food, Canberra, ACT, Australia
| | - Warwick Stiller
- CSIRO Agriculture and Food, Locked, Narrabri, NSW, Australia
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Pengpeng Wang
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology/Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | | | - Iain Wilson
- CSIRO Agriculture and Food, Canberra, ACT, Australia
- Correspondence: and
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33
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Yang H, Zhao T, Jiang J, Wang S, Wang A, Li J, Xu X. Mapping and screening of the tomato Stemphylium lycopersici resistance gene, Sm, based on bulked segregant analysis in combination with genome resequencing. BMC PLANT BIOLOGY 2017; 17:266. [PMID: 29284401 PMCID: PMC5747103 DOI: 10.1186/s12870-017-1215-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/18/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Tomato gray leaf spot disease caused by Stemphylium lycopersici (S. lycopersici) is considered one of the major diseases of cultivated tomatoes. The only S. lycopersici resistance gene, Sm, was derived from the wild tomato species S. pimpinellifolium. Sm has been identified as an effective source of gray leaf spot resistance in tomatoes and has been mapped to tomato chromosome 11. In this study, the first bulked segregant analysis (BSA) combined with genome resequencing for the mapping and screening of the Sm candidate gene was performed. RESULTS Based on the resequencing results, we identified 50,968 Diff-markers, most of which were distributed on chromosome 11. A total of 37 genes were located in the interval of 0.26-Mb. The gene loci of resistant and susceptible lines were sequenced successfully using PCR products. The relative expression levels of candidate genes in resistant and susceptible lines were confirmed via qRT-PCR, Solyc11g011870.1.1 and Solyc11g011880.1.1 were identified through qRT-PCR. A marker, D5, which was cosegregated with the resistant locus, was identified according to the mutation of the Solyc11g011880.1.1 trait in the resistant line. CONCLUSIONS The Sm gene was mapped to the short arm of chromosome 11. The candidate genes Solyc11g011870.1.1 and Solyc11g011880.1.1 displayed expression patterns related to the resistance response. This study will be valuable for Sm cloning and Sm gene breeding in tomato.
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Affiliation(s)
- Huanhuan Yang
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | - Tingting Zhao
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | - Jingbin Jiang
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | | | - Aoxue Wang
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | - Jingfu Li
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China.
| | - Xiangyang Xu
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China.
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Li T, Ma X, Li N, Zhou L, Liu Z, Han H, Gui Y, Bao Y, Chen J, Dai X. Genome-wide association study discovered candidate genes of Verticillium wilt resistance in upland cotton (Gossypium hirsutum L.). PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1520-1532. [PMID: 28371164 PMCID: PMC5698051 DOI: 10.1111/pbi.12734] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/16/2017] [Accepted: 03/21/2017] [Indexed: 05/03/2023]
Abstract
Verticillium wilt (VW), caused by infection by Verticillium dahliae, is considered one of the most yield-limiting diseases in cotton. To examine the genetic architecture of cotton VW resistance, we performed a genome-wide association study (GWAS) using a panel of 299 accessions and 85 630 single nucleotide polymorphisms (SNPs) detected using the specific-locus amplified fragment sequencing (SLAF-seq) approach. Trait-SNP association analysis detected a total of 17 significant SNPs at P < 1.17 × 10-5 (P = 1/85 630, -log10 P = 4.93); the peaks of SNPs associated with VW resistance on A10 were continuous and common in three environments (RDIG2015, RDIF2015 and RDIF2016). Haplotype block structure analysis predicted 22 candidate genes for VW resistance based on A10_99672586 with a minimum P-value (-log10 P = 6.21). One of these genes (CG02) was near the significant SNP A10_99672586 (0.26 Mb), located in a 372-kb haplotype block, and its Arabidopsis AT3G25510 homologues contain TIR-NBS-LRR domains that may be involved in disease resistance response. Real-time quantitative PCR and virus-induced gene silencing (VIGS) analysis showed that CG02 was specific to up-regulation in the resistant (R) genotype Zhongzhimian2 (ZZM2) and that silenced plants were more susceptible to V. dahliae. These results indicate that CG02 is likely the candidate gene for resistance against V. dahliae in cotton. The identified locus or gene may serve as a promising target for genetic engineering and selection for improving resistance to VW in cotton.
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Affiliation(s)
- Tinggang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Xuefeng Ma
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Nanyang Li
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Lei Zhou
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Zheng Liu
- Xinjiang Academy of Agricultural and Reclamation ScienceXinjiangChina
| | - Huanyong Han
- Xinjiang Academy of Agricultural and Reclamation ScienceXinjiangChina
| | - Yuejing Gui
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Yuming Bao
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Jieyin Chen
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
| | - Xiaofeng Dai
- Laboratory of Cotton DiseaseInstitute of Food Science and TechnologyChinese Academy of Agricultural SciencesBeijingChina
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Mei Y, Yu J, Xue A, Fan S, Song M, Pang C, Pei W, Yu S, Zhu J. Dissecting Genetic Network of Fruit Branch Traits in Upland Cotton by Association Mapping Using SSR Markers. PLoS One 2017; 12:e0162815. [PMID: 28121983 PMCID: PMC5266336 DOI: 10.1371/journal.pone.0162815] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/29/2016] [Indexed: 02/04/2023] Open
Abstract
Genetic architecture of branch traits has large influences on the morphological structure, photosynthetic capacity, planting density, and yield of Upland cotton (Gossypium hirsutum L.). This research aims to reveal the genetic effects of six branch traits, including bottom fruit branch node number (BFBNN), bottom fruit branch length (BFBL), middle fruit branch node number (MFBNN), middle fruit branch length (MFBL), upper fruit branch node number (UFBNN), and upper fruit branch length (UFBL). Association mapping was conducted for these traits of 39 lines and their 178 F1 hybrids in three environments. There were 20 highly significant Quantitative Trait SSRs (QTSs) detected by mixed linear model approach analyzing a full genetic model with genetic effects of additive, dominance, epistasis and their environment interaction. The phenotypic variation explained by genetic effects ranged from 32.64 ~ 91.61%, suggesting these branch traits largely influenced by genetic factors.
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Affiliation(s)
- Yongjun Mei
- College of Plant Science, Tarim University, Alar, Xinjiang, China
- * E-mail: (JZ); (YM); (SY)
| | - Jiwen Yu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Angli Xue
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Wenfeng Pei
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Key Laboratory of Cotton Genetic Improvement, Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
- * E-mail: (JZ); (YM); (SY)
| | - Jun Zhu
- Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
- * E-mail: (JZ); (YM); (SY)
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Chen Q, Song J, Du WP, Xu LY, Jiang Y, Zhang J, Xiang XL, Yu GR. Identification, Mapping, and Molecular Marker Development for Rgsr8.1: A New Quantitative Trait Locus Conferring Resistance to Gibberella Stalk Rot in Maize ( Zea mays L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1355. [PMID: 28824686 PMCID: PMC5540892 DOI: 10.3389/fpls.2017.01355] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 05/20/2023]
Abstract
Maize stalk rot is a major fungal disease worldwide, and is difficult to control by chemical methods. Therefore, in maize breeding, quantitative trait loci (QTLs) conferring resistance are important for controlling the disease. Next-generation sequencing technologies are considered a rapid and efficient method to establish the association of agronomic traits with molecular markers or candidate genes. In the present study, we employed QTL-seq, which is a whole-genome resequencing-based approach, to identify candidate genomic regions conferring resistance to maize stalk rot. A novel resistance QTL Rgsr8.1 was finely mapped, conferring broad-spectrum resistance to Gibberella stalk rot (GSR). Segregation analysis in F2 and BC1F1 populations, which were derived from a cross between 18327 (Susceptible) and S72356 (Resistant), indicated that the resistance to GSR was likely to be a quantitatively inherited trait in maize. The result of QTL-seq showed that the resistance to GSR was mapped on chromosome 8 from 161.001 to 170.6 Mb. Based on the simple sequence repeat (SSR) markers, single-nucleotide polymorphism (SNP) markers, and the recombinant test, the location of Rgsr8.1 was narrowed down to 2.04 Mb, flanked by SSR-65 and SNP-25 markers at the physical location from 164.69 to 166.72 Mb based on the maize reference genome. In this region, two candidate resistant genes were found with, one auxin-responsive elements and the other encoding a disease resistance protein. In summary, these results will be useful in maize breeding programs to improve the resistance to GSR in maize.
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Sheng Y, Wang Y, Jiao S, Jin Y, Ji P, Luan F. Mapping and Preliminary Analysis of ABORTED MICROSPORES ( AMS) as the Candidate Gene Underlying the Male Sterility ( MS-5) Mutant in Melon ( Cucumis melo L.). FRONTIERS IN PLANT SCIENCE 2017; 8:902. [PMID: 28611814 PMCID: PMC5447745 DOI: 10.3389/fpls.2017.00902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/15/2017] [Indexed: 05/06/2023]
Abstract
Melon is an important agricultural and economic vegetable crop worldwide. The genetic male sterility mutant (ms-5) has a recessive nuclear gene that controls the male sterility germplasm. Male sterility could reduce the cost of F1 seed production in melon, but heterozygous fertile plants should be removed before pollination. In this study, bulked segregant analysis combined with specific length amplified fragment sequencing was applied to map the single nuclear male sterility recessive gene. A 30-kb candidate region on chromosome 9 located on scaffold 000048 and spanning 2,522,791 to 2,555,104 bp was identified and further confirmed by cleavage amplified polymorphic sequence markers based on parental line resequencing data and classical mapping of 252 F2 individuals. Gene prediction indicated that six annotated genes are present in the 30-kb candidate region. Quantitative RT-PCR revealed significant differences in the expression level of the LOC103498166 ABORTED MICROSPORES (AMS) gene in male-sterile lines (ms-5) and male-fertile (HM1-1) lines during the 2-mm (tetrad) and 5-mm (the first pollen mitosis) periods, and negative regulation of the AMS candidate gene transcription factor was also detected. Sequencing and cluster analysis of the AMS transcription factor revealed five single-nucleotide polymorphisms between the parental lines. The data presented herein suggest that the AMS transcription factor is a possible candidate gene for single nuclear male sterility in melon. The results of this study will help breeders to identify male-sterile and -fertile plants at seeding as marker-assisted selection methods, which would reduce the cost of seed production and improve the use of male-sterile lines in melon.
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Affiliation(s)
- Yunyan Sheng
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural UniversityHarbin, China
- *Correspondence: Yunyan Sheng,
| | - Yudan Wang
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Shiqi Jiao
- Department of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Yazhong Jin
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Peng Ji
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Feishi Luan
- Department of Horticulture, Northeast Agricultural UniversityHarbin, China
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Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection. Sci Rep 2016; 6:38496. [PMID: 27924947 PMCID: PMC5141495 DOI: 10.1038/srep38496] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 11/11/2016] [Indexed: 01/28/2023] Open
Abstract
Fiber quality is one of the most important agronomic traits of cotton, and understanding the genetic basis of its target traits will accelerate improvements to cotton fiber quality. In this study, a panel comprising 355 upland cotton accessions was used to perform genome-wide association studies (GWASs) of five fiber quality traits in four environments. A total of 16, 10 and 7 SNPs were associated with fiber length (FL), fiber strength (FS) and fiber uniformity (FU), respectively, based on the mixed linear model (MLM). Most importantly, two major genomic regions (MGR1 and MGR2) on chromosome Dt7 and four potential candidate genes for FL were identified. Analyzing the geographical distribution of favorable haplotypes (FHs) among these lines revealed that two favorable haplotype frequencies (FHFs) were higher in accessions from low-latitude regions than in accessions from high-latitude regions. However, the genetic diversity of lines from the low-latitude regions was lower than the diversity of lines from the high-latitude regions in China. Furthermore, the FHFs differed among cultivars developed during different breeding periods. These results indicate that FHs have undergone artificial selection during upland cotton breeding in recent decades in China and provide a foundation for the further improvement of fiber quality traits.
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Jia Q, Tan C, Wang J, Zhang XQ, Zhu J, Luo H, Yang J, Westcott S, Broughton S, Moody D, Li C. Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley. BMC Genomics 2016; 17:911. [PMID: 27835941 PMCID: PMC5106812 DOI: 10.1186/s12864-016-3247-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/02/2016] [Indexed: 12/04/2022] Open
Abstract
Background Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. Results We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. Conclusions The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3247-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qiaojun Jia
- College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou, 310018, China. .,Key Laboratory of Plant Secondary Metabolism and Regulation of Zhejiang Province, Hangzhou, 310018, China.
| | - Cong Tan
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Junmei Wang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiao-Qi Zhang
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jinghuan Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Hao Luo
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia
| | - Jianming Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Sharon Westcott
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - Sue Broughton
- Department of Agriculture and Food Government of Western Australia, South Perth, WA, 6155, Australia
| | - David Moody
- InterGrain Pty Ltd, 19 Ambitious Link, Bibra Lake, WA, 6163, Australia
| | - Chengdao Li
- Western Barley Genetics Alliance, Murdoch University, Murdoch, WA, 6150, Australia.
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Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1941-55. [PMID: 26990124 PMCID: PMC5043468 DOI: 10.1111/pbi.12559] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 05/18/2023]
Abstract
Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
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Affiliation(s)
- Cheng Zou
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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McGarry RC, Prewitt SF, Culpepper S, Eshed Y, Lifschitz E, Ayre BG. Monopodial and sympodial branching architecture in cotton is differentially regulated by the Gossypium hirsutum SINGLE FLOWER TRUSS and SELF-PRUNING orthologs. THE NEW PHYTOLOGIST 2016; 212:244-58. [PMID: 27292411 DOI: 10.1111/nph.14037] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 04/26/2016] [Indexed: 05/08/2023]
Abstract
Domestication of upland cotton (Gossypium hirsutum) converted it from a lanky photoperiodic perennial to a day-neutral annual row-crop. Residual perennial traits, however, complicate irrigation and crop management, and more determinate architectures are desired. Cotton simultaneously maintains robust monopodial indeterminate shoots and sympodial determinate shoots. We questioned if and how the FLOWERING LOCUS T/SINGLE FLOWER TRUSS (SFT)-like and TERMINAL FLOWER1/SELF-PRUNING (SP)-like genes control the balance of monopodial and sympodial growth in a woody perennial with complex growth habit. Virus-based manipulation of GhSP and GhSFT expression enabled unprecedented functional analysis of cotton development. GhSP maintains growth in all apices; in its absence, both monopodial and sympodial branch systems terminate precociously. GhSFT encodes a florigenic signal stimulating rapid onset of sympodial branching and flowering in side shoots of wild photoperiodic and modern day-neutral accessions. High florigen concentrations did not alter monopodial apices, implying that once a cotton apex is SP-determined, it cannot be reset by florigen. GhSP is also essential to establish and maintain cambial activity. Dynamic changes in GhSFT and GhSP levels navigate meristems between monopodial and sympodial programs in a single plant. SFT and SP influenced cotton domestication and are ideal targets for further agricultural optimization.
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Affiliation(s)
- Roisin C McGarry
- Department of Biological Sciences, University of North Texas, 1155 Union Circle 305220, Denton, TX, 76203-5017, USA
| | - Sarah F Prewitt
- Department of Biological Sciences, University of North Texas, 1155 Union Circle 305220, Denton, TX, 76203-5017, USA
| | - Samantha Culpepper
- Department of Biological Sciences, University of North Texas, 1155 Union Circle 305220, Denton, TX, 76203-5017, USA
| | - Yuval Eshed
- Plant Sciences, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Eliezer Lifschitz
- Department of Biology, Technion - Israel Institute of Technology, Haifa, 3200003, Israel
| | - Brian G Ayre
- Department of Biological Sciences, University of North Texas, 1155 Union Circle 305220, Denton, TX, 76203-5017, USA
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Zheng W, Wang Y, Wang L, Ma Z, Zhao J, Wang P, Zhang L, Liu Z, Lu X. Genetic mapping and molecular marker development for Pi65(t), a novel broad-spectrum resistance gene to rice blast using next-generation sequencing. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1035-44. [PMID: 26883042 DOI: 10.1007/s00122-016-2681-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 01/23/2016] [Indexed: 05/17/2023]
Abstract
A novel R gene was mapped to a locus on chromosome 11 from 30.42 to 30.85 Mb, which was proven to be efficient in the improvement of rice blast resistance. Rice blast is a devastating fungal disease worldwide. The use of blast resistance (R) genes is the most important approach to control the disease in rice breeding. In the present study, we finely mapped a novel resistance gene Pi65(t), conferring a broad-spectrum resistance to the fungus Magnaporthe oryzae, using bulked segregant analysis in combination with next-generation sequencing technology. Segregation in a doubled haploid (DH) population and a BC1F2 population suggested that resistance to blast in Gangyu129 was likely conferred by a single dominant gene, designated Pi65(t); it was located on chromosome 11 from 30.20 to 31.20 Mb using next-generation sequencing. After screening recombinants with newly developed molecular markers, the region was narrowed down to 0.43 Mb, flanked by SNP-2 and SNP-8 at the physical location from 30.42 to 30.85 Mb based on the Nipponbare reference database in build 5. Using the software QTL IciMapping, Pi65(t) was further mapped to a locus between InDel-1 and SNP-4 with genetic distances of 0.11 and 0.98 cM, respectively. Within this region, 4 predicted R genes were found with nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. We developed molecular markers to genotype 305 DH lines and found that InDel-1 was closely linked with Pi65(t). Using InDel-1, a new rice variety Chuangxin1 containing Pi65(t) was developed, and it is highly resistant to rice blast and produces a high yield in Liaoning province of China. This indicated that Pi65(t) could play a key role in the improvement of rice blast resistance.
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Affiliation(s)
- Wenjing Zheng
- Crops Molecular Improvement Laboratory, Liaoning Innovation Center of the Academy of Agricultural Sciences, 84 Dongling Road, Shenyang, 110161, China.
| | - Yan Wang
- Plant Protection College, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110161, China
| | - Lili Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110161, China
| | - Zuobin Ma
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110161, China
| | - Jiaming Zhao
- Crops Molecular Improvement Laboratory, Liaoning Innovation Center of the Academy of Agricultural Sciences, 84 Dongling Road, Shenyang, 110161, China
| | - Ping Wang
- Crops Molecular Improvement Laboratory, Liaoning Innovation Center of the Academy of Agricultural Sciences, 84 Dongling Road, Shenyang, 110161, China
| | - Lixia Zhang
- Crops Molecular Improvement Laboratory, Liaoning Innovation Center of the Academy of Agricultural Sciences, 84 Dongling Road, Shenyang, 110161, China
| | - Zhiheng Liu
- Plant Protection College, Shenyang Agricultural University, 120 Dongling Road, Shenyang, 110161, China
| | - Xiaochun Lu
- Crops Molecular Improvement Laboratory, Liaoning Innovation Center of the Academy of Agricultural Sciences, 84 Dongling Road, Shenyang, 110161, China.
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To Be a Flower or Fruiting Branch: Insights Revealed by mRNA and Small RNA Transcriptomes from Different Cotton Developmental Stages. Sci Rep 2016; 6:23212. [PMID: 26983497 PMCID: PMC4794708 DOI: 10.1038/srep23212] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 03/02/2016] [Indexed: 12/14/2022] Open
Abstract
The architecture of the cotton plant, including fruit branch formation and flowering pattern, is the most important characteristic that directly influences light exploitation, yield and cost of planting. Nulliplex branch is a useful phenotype to study cotton architecture. We used RNA sequencing to obtain mRNA and miRNA profiles from nulliplex- and normal-branch cotton at three developmental stages. The differentially expressed genes (DEGs) and miRNAs were identified that preferentially/specifically expressed in the pre-squaring stage, which is a key stage controlling the transition from vegetative to reproductive growth. The DEGs identified were primarily enriched in RNA, protein, and signalling categories in Gossypium barbadense and Gossypium hirsutum. Interestingly, during the pre-squaring stage, the DEGs were predominantly enriched in transcription factors in both G. barbadense and G. hirsutum, and these transcription factors were mainly involved in branching and flowering. Related miRNAs were also identified. The results showed that fruit branching in cotton is controlled by molecular pathways similar to those in Arabidopsis and that multiple regulated pathways may affect the development of floral buds. Our study showed that the development of fruit branches is closely related to flowering induction and provides insight into the molecular mechanisms of branch and flower development in cotton.
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Su J, Fan S, Li L, Wei H, Wang C, Wang H, Song M, Zhang C, Gu L, Zhao S, Mao G, Wang C, Pang C, Yu S. Detection of Favorable QTL Alleles and Candidate Genes for Lint Percentage by GWAS in Chinese Upland Cotton. FRONTIERS IN PLANT SCIENCE 2016; 7:1576. [PMID: 27818672 PMCID: PMC5073211 DOI: 10.3389/fpls.2016.01576] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 10/06/2016] [Indexed: 05/18/2023]
Abstract
Improving cotton yield is a major breeding goal for Chinese upland cotton. Lint percentage is an important yield component and a critical economic index for cotton cultivars, and raising the lint percentage has a close relationship to improving cotton lint yield. To investigate the genetic architecture of lint percentage, a diversity panel consisting of 355 upland cotton accessions was grown, and the lint percentage was measured in four different environments. Genotyping was performed with specific-locus amplified fragment sequencing (SLAF-seq). Twelve single-nucleotide polymorphisms (SNPs) associated with lint percentage were detected via a genome-wide association study (GWAS), in which five SNP loci distributed on chromosomes At3 (A02) and At4 (A08) and contained two major-effect QTLs, which were detected in the best linear unbiased predictions (BLUPs) and in more than three environments simultaneously. Furthermore, favorable haplotypes (FHs) of two major-effect QTLs and 47 putative candidate genes in the two linkage disequilibrium (LD) blocks of these associated loci were identified. The expression levels of these putative candidate genes were estimated using RNA-seq data from ten upland cotton tissues. We found that Gh_A02G1268 was very highly expressed during the early fiber development stage, whereas the gene was poorly expressed in the seed. These results implied that Gh_A02G1268 may determine the lint percentage by regulating seed and fiber development. The favorable QTL alleles and candidate genes for lint percentage identified in this study will have high potential for improving lint yield in future Chinese cotton breeding programs.
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Affiliation(s)
- Junji Su
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
- Department of Plant Sciences, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Libei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Hengling Wei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Caixiang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Hantao Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Chi Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Lijiao Gu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Shuqi Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Guangzhi Mao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
| | - Chengshe Wang
- Department of Plant Sciences, College of Agronomy, Northwest A&F UniversityYangling, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
- *Correspondence: Chaoyou Pang
| | - Shuxun Yu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of CAASAnyang, China
- Department of Plant Sciences, College of Agronomy, Northwest A&F UniversityYangling, China
- Shuxun Yu
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Characterization and fine mapping of a novel barley Stage Green-Revertible Albino Gene (HvSGRA) by Bulked Segregant Analysis based on SSR assay and Specific Length Amplified Fragment Sequencing. BMC Genomics 2015; 16:838. [PMID: 26494145 PMCID: PMC4619012 DOI: 10.1186/s12864-015-2015-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 10/06/2015] [Indexed: 11/28/2022] Open
Abstract
Background Leaf color variations are common in plants. Herein we describe a natural mutant of barley cultivar Edamai No.6, whs18, whose leaf color showed stable and inheritable stage-green-revertible-albino under field condition. Methods Bulked Segregant Analysis (BSA) based on SSR assay and Specific Length Amplified Fragment Sequencing (SLAF-seq) was used to map the candidate gene for this trait. Results We found that leaf color of whs18 was green at seedling stage, while the seventh or eighth leaf began to show etiolation, and albino leaves emerged after a short period. The newly emerged leaves began to show stripe white before jointing stage, and normal green leaves emerged gradually. The duration of whs18 with abnormal leaf color lasted for about 3 months, which had some negative impacts on yield-related-traits. Further investigations showed that the variation was associated with changes in chlorophyII content and chloroplast development. Genetic analysis revealed that the trait was controlled by a single recessive nuclear gene, and was designed as HvSGRA in this study. Based on the F2 population derived from Edamai No.9706 and whs18, we initially mapped the HvSGRA gene on the short arm of chromosome 2H using SSR and BSA. GBMS247 on 2HS showed co-segregation with HvSGRA. The genetic distance between the other marker GBM1187 and HvSGRA was 1.2 cM. Further analysis using BSA with SLAF-seq also identified this region as candidate region. Finally, HvSGRA interval was narrowed to 0.4 cM between morex_contig_160447 and morex_contig_92239, which were anchored to two adjacent FP contigs, contig_34437 and contig_46434, respectively. Furthermore, six putative genes with high-confidence in this interval were identified by POPSEQ. Further analysis showed that the substitution from C to A in the third exon of fructokinase-1-like gene generated a premature stop codon in whs18, which may lead to loss function of this gene. Conclusions Using SSR and SLAF-seq in conjunction with BSA, we mapped HvSGRA within two adjacent FP contigs of barley. The mutation of fructokinase-1-like gene in whs18 may cause the stage green-revertible albino of barley. The current study lays foundation for hierarchical map-based cloning of HvSGRA and utilizing the gene/trait as a visualized maker in molecular breeding in future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2015-1) contains supplementary material, which is available to authorized users.
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