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Li S, Kong L, Xiao X, Li P, Liu A, Li J, Gong J, Gong W, Ge Q, Shang H, Pan J, Chen H, Peng Y, Zhang Y, Lu Q, Shi Y, Yuan Y. Genome-wide artificial introgressions of Gossypium barbadense into G. hirsutum reveal superior loci for simultaneous improvement of cotton fiber quality and yield traits. J Adv Res 2023; 53:1-16. [PMID: 36460274 PMCID: PMC10658236 DOI: 10.1016/j.jare.2022.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 10/31/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
INTRODUCTION The simultaneous improvement of fiber quality and yield for cotton is strongly limited by the narrow genetic backgrounds of Gossypium hirsutum (Gh) and the negative genetic correlations among traits. An effective way to overcome the bottlenecks is to introgress the favorable alleles of Gossypium barbadense (Gb) for fiber quality into Gh with high yield. OBJECTIVES This study was to identify superior loci for the improvement of fiber quality and yield. METHODS Two sets of chromosome segment substitution lines (CSSLs) were generated by crossing Hai1 (Gb, donor-parent) with cultivar CCRI36 (Gh) and CCRI45 (Gh) as genetic backgrounds, and cultivated in 6 and 8 environments, respectively. The kmer genotyping strategy was improved and applied to the population genetic analysis of 743 genomic sequencing data. A progeny segregating population was constructed to validate genetic effects of the candidate loci. RESULTS A total of 68,912 and 83,352 genome-wide introgressed kmers were identified in the CCRI36 and CCRI45 populations, respectively. Over 90 % introgressions were homologous exchanges and about 21 % were reverse insertions. In total, 291 major introgressed segments were identified with stable genetic effects, of which 66(22.98 %), 64(21.99 %), 35(12.03 %), 31(10.65 %) and 18(6.19 %) were beneficial for the improvement of fiber length (FL), strength (FS), micronaire, lint-percentage (LP) and boll-weight, respectively. Thirty-nine introgression segments were detected with stable favorable additive effects for simultaneous improvement of 2 or more traits in Gh genetic background, including 6 could increase FL/FS and LP. The pyramiding effects of 3 pleiotropic segments (A07:C45Clu-081, D06:C45Clu-218, D02:C45Clu-193) were further validated in the segregating population. CONCLUSION The combining of genome-wide introgressions and kmer genotyping strategy showed significant advantages in exploring genetic resources. Through the genome-wide comprehensive mining, a total of 11 clusters (segments) were discovered for the stable simultaneous improvement of FL/FS and LP, which should be paid more attention in the future.
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Affiliation(s)
- Shaoqi Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Linglei Kong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xianghui Xiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Pengtao Li
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Junwen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Juwu Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Jingtao Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hong Chen
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi 832000, China
| | - Yan Peng
- Third Division of the Xinjiang Production and Construction Corps Agricultural Research Institute, Tumushuke 843900, China
| | - Yuanming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Quanwei Lu
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang 455000, China.
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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Bao Y, Wei Y, Liu Y, Gao J, Cheng S, Liu G, You Q, Liu P, Lu Q, Li P, Zhang S, Hu N, Han Y, Liu S, Wu Y, Yang Q, Li Z, Ao G, Liu F, Wang K, Jiang J, Zhang T, Zhang W, Peng R. Genome-wide chromatin accessibility landscape and dynamics of transcription factor networks during ovule and fiber development in cotton. BMC Biol 2023; 21:165. [PMID: 37525156 PMCID: PMC10391996 DOI: 10.1186/s12915-023-01665-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 07/18/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The development of cotton fiber is regulated by the orchestrated binding of regulatory proteins to cis-regulatory elements associated with developmental genes. The cis-trans regulatory dynamics occurred throughout the course of cotton fiber development are elusive. Here we generated genome-wide high-resolution DNase I hypersensitive sites (DHSs) maps to understand the regulatory mechanisms of cotton ovule and fiber development. RESULTS We generated DNase I hypersensitive site (DHS) profiles from cotton ovules at 0 and 3 days post anthesis (DPA) and fibers at 8, 12, 15, and 18 DPA. We obtained a total of 1185 million reads and identified a total of 199,351 DHSs through ~ 30% unique mapping reads. It should be noted that more than half of DNase-seq reads mapped multiple genome locations and were not analyzed in order to achieve a high specificity of peak profile and to avoid bias from repetitive genomic regions. Distinct chromatin accessibilities were observed in the ovules (0 and 3 DPA) compared to the fiber elongation stages (8, 12, 15, and 18 DPA). Besides, the chromatin accessibility during ovules was particularly elevated in genomic regions enriched with transposable elements (TEs) and genes in TE-enriched regions were involved in ovule cell division. We analyzed cis-regulatory modules and revealed the influence of hormones on fiber development from the regulatory divergence of transcription factor (TF) motifs. Finally, we constructed a reliable regulatory network of TFs related to ovule and fiber development based on chromatin accessibility and gene co-expression network. From this network, we discovered a novel TF, WRKY46, which may shape fiber development by regulating the lignin content. CONCLUSIONS Our results not only reveal the contribution of TEs in fiber development, but also predict and validate the TFs related to fiber development, which will benefit the research of cotton fiber molecular breeding.
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Affiliation(s)
- Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Jingjing Gao
- National Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored By Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China
| | - Shuang Cheng
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Qi You
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Peng Liu
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, 225009, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Pengtao Li
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Shulin Zhang
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Nan Hu
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Shuo Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Qingqing Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Zhaoguo Li
- Anyang Institute of Technology, Anyang, Henan, 455000, China
- Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Guowei Ao
- Anyang Institute of Technology, Anyang, Henan, 455000, China
| | - Fang Liu
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Kunbo Wang
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China
| | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
- Michigan State University AgBioResearch, East Lansing, MI, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Agricultural College of Yangzhou University, Yangzhou, 225009, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China.
| | - Wenli Zhang
- National Key Laboratory for Crop Genetics and Germplasm Enhancement and Utilization, Collaborative Innovation Center for Modern Crop Production Co-Sponsored By Province and Ministry (CIC-MCP), Nanjing Agricultural University, No.1 Weigang, Nanjing, 210095, Jiangsu, China.
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, 455000, China.
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Anyang, Henan, 455000, China.
- Zhengzhou University, Zhengzhou, Henan, 450001, China.
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Wang S, Wu H, Zhao Y, Wang L, Guan X, Zhao T. Mapping intron retention events contributing to complex traits using splice quantitative trait locus. Plant Methods 2023; 19:72. [PMID: 37480119 PMCID: PMC10362629 DOI: 10.1186/s13007-023-01048-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 07/03/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Alternative splicing (AS) of mRNA plays an important roles in transcriptome diversity, involving regulation of plant growth and stress response. Understanding the variation of AS events underlying GWAS loci in a crop population can provide insight into the molecular mechanisms of complex agronomic traits. To date, genome-wide association studies relating AS events to agronomic traits have rarely been conducted at the population level in crops. RESULTS Here, a pipeline was constructed to identify candidate AS events related to complex traits. Firstly, ovule transcriptome data were used to characterize intron retention (IR), the predominant type of AS in plants, on a genome-wide scale. This was done in a natural population consisting of 279 upland cotton lines. Secondly, splice quantitative trait locus (sQTL) analysis was carried out, which yielded a total of 2295 sQTLs involving 1607 genes. Of these, 14.25% (n = 427) were cis-regulatory loci. Integration with expression quantitative trait loci (eQTL) revealed that 53 (21.4%) cis-sGenes were regulated by both cis-sQTLs and cis-eQTLs. Finally, co-localization analysis integrated with GWAS loci in this population showed 32 cis-QTLs to be co-located with genetic regulatory loci related to fiber yield and quality traits, indicating that sQTLs are likely to participate in regulating cotton fiber yield and quality. An in-depth evaluation confirmed that differences in the IR rates of sQTL-regulated candidate genes such as GhLRRK1 and GhGC1 are associated with lint percentage (LP), which has potential in breeding applications. CONCLUSION This study provides a clue that AS of mRNA has an impact on crop yield, along with functional sQTLs are new genetic resources for cotton precision breeding.
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Affiliation(s)
- Siyuan Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
| | - Hongyu Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
| | - Yongyan Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China
| | - Luyao Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China.
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China.
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China.
- Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China.
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Niu H, Kuang M, Huang L, Shang H, Yuan Y, Ge Q. Lint percentage and boll weight QTLs in three excellent upland cotton (Gossypium hirsutum): ZR014121, CCRI60, and EZ60. BMC Plant Biol 2023; 23:179. [PMID: 37020180 PMCID: PMC10074700 DOI: 10.1186/s12870-023-04147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield. RESULTS Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation. CONCLUSIONS A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Kuang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Longyu Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Li Y, Si Z, Wang G, Shi Z, Chen J, Qi G, Jin S, Han Z, Gao W, Tian Y, Mao Y, Fang L, Hu Y, Chen H, Zhu X, Zhang T. Genomic insights into the genetic basis of cotton breeding in China. Mol Plant 2023; 16:662-677. [PMID: 36738104 DOI: 10.1016/j.molp.2023.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The excellent Upland cotton (Gossypium hirsutum) cultivars developed since 1949 have made a huge contribution to cotton production in China, the world's largest producer and consumer of cotton. However, the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear. In this study, we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent, advanced generation, intercross (MAGIC) population comprising 920 recombinant inbred lines. A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality. Of them, 25 (46.30%) pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits, revealing complex trade-offs and linkage drags in Upland cotton agronomic traits. Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles. Interestingly, 85% of these elite alleles were selected and fixed from different American ancestors, consistent with cotton breeding practices in China. However, seven elite alleles of native origin that are responsible for Fusarium wilt resistance, early maturing, good-quality fiber, and other characteristics were not found in American ancestors but have greatly contributed to Chinese cotton breeding and wide cultivation. Taken together, these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.
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Affiliation(s)
- Yiqian Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoping Wang
- Xinjiang Production and Construction Corps Seventh Division Agricultural Research Institute, Kuintun, China
| | - Zhuolin Shi
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoan Qi
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shangkun Jin
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wenhao Gao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yue Tian
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China; College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Yun Mao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hong Chen
- Key Laboratory of China Northwestern Inland Region, Ministry of Agriculture, Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Xiefei Zhu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Tianzhen Zhang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, the Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
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Tian Y, Li D, Wang X, Zhang H, Wang J, Yu L, Guo C, Luan X, Liu X, Li H, Reif JC, Li YH, Qiu LJ. Deciphering the genetic basis of resistance to soybean cyst nematode combining IBD and association mapping. Theor Appl Genet 2023; 136:50. [PMID: 36912956 PMCID: PMC10011322 DOI: 10.1007/s00122-023-04268-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 12/07/2022] [Indexed: 06/18/2023]
Abstract
IBD analysis clarified the dynamics of chromosomal recombination during the ZP pedigree breeding process and identified ten genomic regions resistant to SCN race3 combining association mapping. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pathogens for soybean production worldwide. The cultivar Zhongpin03-5373 (ZP), derived from SCN-resistant progenitor parents, Peking, PI 437654 and Huipizhi Heidou, is an elite line with high resistance to SCN race3. In the current study, a pedigree variation map was generated for ZP and its ten progenitors using 3,025,264 high-quality SNPs identified from an average of 16.2 × re-sequencing for each genome. Through identity by decent (IBD) tracking, we showed the dynamic change of genome and detected important IBD fragments, which revealed the comprehensively artificial selection of important traits during ZP breeding process. A total of 2,353 IBD fragments related to SCN resistance including SCN-resistant genes rhg1, rhg4 and NSFRAN07 were identified based on the resistant-related genetic paths. Moreover, 23 genomic regions underlying resistance to SCN race3 were identified by genome-wide association study (GWAS) in 481 re-sequenced cultivated soybeans. Ten common loci were found by both IBD tracking and GWAS analysis. Haplotype analysis of 16 potential candidate genes suggested a causative SNP (C/T, - 1065) located in the promoter of Glyma.08G096500 and encoding a predicted TIFY5b-related protein on chr8 was highly correlated with SCN race3 resistance. Our results more thoroughly elucidated the dynamics of genomic fragments during ZP pedigree breeding and the genetic basis of SCN resistance, which will provide useful information for gene cloning and the development of resistant soybean cultivars using a marker-assisted selection approach.
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Affiliation(s)
- Yu Tian
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Delin Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Xueqing Wang
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Hao Zhang
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Jiajun Wang
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Lijie Yu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Heilongjiang Province, Harbin, China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Heilongjiang Province, Harbin, China
| | - Xiaoyan Luan
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xinlei Liu
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Hongjie Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China
| | - Jochen C Reif
- Department of Breeding Research, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ying-Hui Li
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
| | - Li-Juan Qiu
- The National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Science, Beijing, 100081, People's Republic of China.
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7
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Shen Q, Zhang S, Ge C, Liu S, Chen J, Liu R, Ma H, Song M, Pang C. Genome-wide association study identifies GhSAL1 affects cold tolerance at the seedling emergence stage in upland cotton (Gossypium hirsutum L.). Theor Appl Genet 2023; 136:27. [PMID: 36810826 DOI: 10.1007/s00122-023-04317-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Genomic analysis of upland cotton revealed that cold tolerance was associated with ecological distribution. GhSAL1 on chromosome D09 negatively regulated cold tolerance of upland cotton. Cotton can undergo low-temperature stress at the seedling emergence stage, which adversely affects growth and yield; however, the regulatory mechanism underlying cold tolerance remains nebulous. Here, we analyze the phenotypic and physiological parameters in 200 accessions from 5 ecological distributions under constant chilling (CC) and diurnal variation of chilling (DVC) stresses at the seedling emergence stage. All accessions were clustered into four groups, of which Group IV, with most germplasms from the northwest inland region (NIR), had better phenotypes than Groups I-III under the two kinds of chilling stresses. A total of 575 significantly associated single-nucleotide polymorphism (SNP) were identified, and 35 stable genetic quantitative trait loci (QTL) were obtained, of which 5 were associated with traits under CC and DVC stress, respectively, while the remaining 25 were co-associated. The accumulation of dry weight (DW) of seedling was associated with the flavonoid biosynthesis process regulated by Gh_A10G0500. The emergence rate (ER), DW, and total length of seedling (TL) under CC stress were associated with the SNPs variation of Gh_D09G0189 (GhSAL1). GhSAL1HapB was the elite haplotype, which increased ER, DW, and TL by 19.04%, 11.26%, and 7.69%, respectively, compared with that of GhSAL1HapA. The results of virus-induced gene silencing (VIGS) experiment and determination of metabolic substrate content preliminarily illustrated that GhSAL1 negatively regulated cotton cold tolerance through IP3-Ca2+ signaling pathway. The elite haplotypes and candidate genes identified in this study could be used to improve cold tolerance at the seedling emergence stage in future upland cotton breeding.
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Affiliation(s)
- Qian Shen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- MOA Key Laboratory of Crop Eco-physiology and Farming system in the Middle Reaches of Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430000, Hubei, China
| | - Siping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Changwei Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Shaodong Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Jing Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ruihua Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Huijuan Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meizhen Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
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He GQ, Huang XX, Pei MS, Jin HY, Cheng YZ, Wei TL, Liu HN, Yu YH, Guo DL. Dissection of the Pearl of Csaba pedigree identifies key genomic segments related to early ripening in grape. Plant Physiol 2023; 191:1153-1166. [PMID: 36440478 PMCID: PMC9922404 DOI: 10.1093/plphys/kiac539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Pearl of Csaba (PC) is a valuable backbone parent for early-ripening grapevine (Vitis vinifera) breeding, from which many excellent early ripening varieties have been bred. However, the genetic basis of the stable inheritance of its early ripening trait remains largely unknown. Here, the pedigree, consisting of 40 varieties derived from PC, was re-sequenced for an average depth of ∼30×. Combined with the resequencing data of 24 other late-ripening varieties, 5,795,881 high-quality single nucleotide polymorphisms (SNPs) were identified following a strict filtering pipeline. The population genetic analysis showed that these varieties could be distinguished clearly, and the pedigree was characterized by lower nucleotide diversity and stronger linkage disequilibrium than the non-pedigree varieties. The conserved haplotypes (CHs) transmitted in the pedigree were obtained via identity-by-descent analysis. Subsequently, the key genomic segments were identified based on the combination analysis of haplotypes, selective signatures, known ripening-related quantitative trait loci (QTLs), and transcriptomic data. The results demonstrated that varieties with a superior haplotype, H1, significantly (one-way ANOVA, P < 0.001) exhibited early grapevine berry development. Further analyses indicated that H1 encompassed VIT_16s0039g00720 encoding a folate/biopterin transporter protein (VvFBT) with a missense mutation. VvFBT was specifically and highly expressed during grapevine berry development, particularly at veraison. Exogenous folate treatment advanced the veraison of "Kyoho". This work uncovered core haplotypes and genomic segments related to the early ripening trait of PC and provided an important reference for the molecular breeding of early-ripening grapevine varieties.
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Affiliation(s)
- Guang-Qi He
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, China
| | - Xi-Xi Huang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
| | - Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, China
| | - Hui-Ying Jin
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, China
| | - Yi-Zhe Cheng
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, China
| | - Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, China
| | - Da-Long Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Henan University of Science and Technology, Luoyang 471023, 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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Liu WL, Zhao JB, Zeng H, Wan CX. Effect of polyaspartic acid on soil water storage, soil microbial diversity, cotton yield and fiber quality. Arch Microbiol 2022; 205:35. [PMID: 36562907 DOI: 10.1007/s00203-022-03375-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Water-saving is one of the most important problems in agricultural development, especially in arid and semi-arid areas. The effects of polyaspartic acid (PASP) on soil water storage, soil microbial community, soil physiochemical properties, cotton yield and fiber quality were studied to find water-saving material utilized in cotton field. The experiment was divided into two parts, the first part concerned the direct application of three different amounts of PASP under field conditions. In the second part, PASP was mixed with soil in different proportions and the mixtures were put into bottles, which were then buried in the cotton field. The application of PASP improved the water-holding capacity and thus increased water content available to the cotton root system in the cotton field for a long time, and significantly (p < 0.05) increased the content of soil organic matter, available P and ammonium-N. Relative abundances of Methylophaga, Sphingomonas, Cupriavidus, Pseudeurotium, Fusarium and Nectria were significantly affected by applying PASP. Compared to the control group, 15, 75 and 150 kg ha-1 of PASP increased seed cotton yield by 3.94, 8.31 and 7.71%, respectively. The application of PASP also increased the reflectance degree, Micronaire and short fiber index of cotton. These results suggested that 75 kg ha-1 of PASP can be appropriate to alleviate drought stress in arid and semi-arid areas.
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Affiliation(s)
- Wen-Long Liu
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China
| | - Jian-Bo Zhao
- Beijing Key Lab of Bioprocess in Beijing University of Chemical Technology, 100029, Beijing, People's Republic of China
| | - Hong Zeng
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China.
| | - Chuan-Xing Wan
- Xinjiang Production and Construction Corps Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, College of Life Science, Tarim University, Alar, 843300, Xinjiang, People's Republic of China.
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11
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Chen H, Han Z, Ma Q, Dong C, Ning X, Li J, Lin H, Xu S, Li Y, Hu Y, Si Z, Song Q. Identification of elite fiber quality loci in upland cotton based on the genotyping-by-target-sequencing technology. Front Plant Sci 2022; 13:1027806. [PMID: 36407612 PMCID: PMC9669494 DOI: 10.3389/fpls.2022.1027806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Genome-wide association studies (GWAS) of fiber quality traits of upland cotton were conducted to identify the single-nucleotide polymorphic (SNP) loci associated with cotton fiber quality, which lays the foundation for the mining of elite] cotton fiber gene resources and its application in molecular breeding. A total of 612 upland cotton accessions were genotyped using the ZJU Cotton Chip No. 1 40K chip array via the liquid-phase probe hybridization-based genotyping-by-target-sequencing (GBTS) technology. In the present study, five fiber quality traits, namely fiber length, fiber strength, micronaire, uniformity and elongation, showed different degrees of variation in different environments. The average coefficient of variation of fiber strength was the greatest, whereas the average coefficient of variation of uniformity was the least. Significant or extremely significant correlations existed among the five fiber quality traits, especially fiber length, strength, uniformity and elongation all being significantly negative correlated with micronaire. Population cluster analysis divided the 612 accessions into four groups: 73 assigned to group I, 226 to group II, 220 to group III and 93 to group IV. Genome-wide association studies of five fiber quality traits in five environments was performed and a total of 42 SNP loci associated with target traits was detected, distributed on 19 chromosomes, with eight loci associated with fiber length, five loci associated with fiber strength, four loci associated with micronaire, twelve loci associated with fiber uniformity and thirteen loci associated with fiber elongation. Of them, seven loci were detected in more than two environments. Nine SNP loci related to fiber length, fiber strength, uniformity and elongation were found on chromosome A07, seven loci related to fiber length, fiber strength, micronaire and elongation were detected on chromosome D01, and five loci associated with fiber length, uniformity and micronaire were detected on chromosome D11. The results from this study could provide more precise molecular markers and genetic resources for cotton breeding for better fiber quality in the future.
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Affiliation(s)
- Hong Chen
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
| | - Zegang Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Research Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qi Ma
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
| | - Chengguang Dong
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
| | - Xinzhu Ning
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
| | - Jilian Li
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
| | - Hai Lin
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
| | - Shouzhen Xu
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
| | - Yiqian Li
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Research Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Research Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Research Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qingping Song
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Northwest Inland Region Key Laboratory of Cotton Biology and Genetic Breeding of Ministry of Agriculture, Shihezi, China
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12
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Dong J, Zhou K, Ge X, Xu N, Wang X, He Q, Zhang C, Chu J, Li Q. Effects of Extraction Technique on the Content and Antioxidant Activity of Flavonoids from Gossypium Hirsutum linn. Flowers. Molecules 2022; 27:molecules27175627. [PMID: 36080389 PMCID: PMC9458133 DOI: 10.3390/molecules27175627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/19/2022] [Accepted: 08/26/2022] [Indexed: 11/28/2022] Open
Abstract
Cotton is one of the Uyghur medical materials in China and is rich in flavonoids. Flavonoids have important pharmacological effects. The yield of flavonoids in traditional extraction methods is low, which affects the development of flavonoids. Therefore, it is urgent to optimize the extraction techniques. The yield of flavonoids in cotton flowers was effectively improved by response surface methodology, and the highest yield of flavonoids reached 5.66%, and the optimal extraction process conditions were obtained. The DPPH free radical scavenging rate, hydroxyl free radical scavenging rate, superoxide anion free radical scavenging rate, and reducing ability were tested to reflect the antioxidant capacity of flavonoids. The flavonoids had an excellent antioxidant effect. Cell experiments suggested that the flavonoids had the effect of protecting glutamate-induced damage to HT-22 cells. The results of this study provide a theoretical basis for the extraction of cotton flowers flavonoids and the comprehensive evaluation of antioxidant products, as well as the extraction of other plant flavonoids.
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Affiliation(s)
- Jiaxing Dong
- Key Laboratory of Xi’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
- Research and Technology Center, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Kehai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences (CAAS), Anyang 455000, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agriculture Sciences (CAAS), Anyang 455000, China
| | - Na Xu
- State Key Laboratory of Tea Plant Biology and Utilization, School of Tea & Food Science and International Joint Laboratory on Tea Chemistry and Health Effects of Ministry of Education, Anhui Agricultural University, Hefei 230036, China
| | - Xiao Wang
- Key Laboratory of Xi’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Qing He
- Key Laboratory of Xi’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
- Research and Technology Center, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Chenxu Zhang
- Key Laboratory of Xi’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
- Research and Technology Center, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Jun Chu
- Key Laboratory of Xi’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
- Research and Technology Center, Anhui University of Chinese Medicine, Hefei 230038, China
- Correspondence: (J.C.); (Q.L.)
| | - Qinglin Li
- Key Laboratory of Xi’an Medicine, Ministry of Education, Anhui University of Chinese Medicine, Hefei 230038, China
- Research and Technology Center, Anhui University of Chinese Medicine, Hefei 230038, China
- Correspondence: (J.C.); (Q.L.)
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Liu Y, Nazir MF, He S, Li H, Pan Z, Sun G, Dai P, Wang L, Du X. Deltapine 15 contributes to the genomic architecture of modern upland cotton cultivars. Theor Appl Genet 2022; 135:1401-1411. [PMID: 35146550 DOI: 10.1007/s00122-022-04042-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/22/2022] [Indexed: 06/14/2023]
Abstract
Foundation parents play a critical role in the genetic constituents of the derived genotypes. Deltapine-15 (DLP-15), introduced to China in 1950, is one of the most commonly used parents for early breeding programs in China. However, the formation and inheritance patterns of genomic constituents have not been studied. Therefore, this study aimed at understanding and exploring the genomic architecture of 146 DLP-15 derived cultivars with a common foundation parent DLP-15. Population structure based on sequencing data clustered genotypes into two groups (G1 and G2) supported by principal component analysis. Further exploration led to the identification of Chr-A08 with significantly differentiated regions between two groups. Moreover, we identified genome-wide identity by descent (IBD) segments (840 segments) to understand the genomic inheritance pattern in DLP-15 derived cultivars, spanning the 20-95 Mb region on Chr-A08. Interestingly, Chr-A08 depicted a unique inheritance pattern from DLP-15 to its derived cultivars. IBD-segment-based haplotype analysis suggested significant differences among the two groups. Phenotypic trait association with DLP-derived haplotypes concerning Chr-A08 suggested a significant increase in yield and fiber quality. Furthermore, distinguished IBD segments overlapped with previously reported QTLs concerning fiber yield and quality. Our results systematically identified genomic signatures transmitted from the foundation parent DLP-15 to its derived cultivars and provided a basis for further exploiting excellent haplotypes associated with DLP-15.
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Affiliation(s)
- Yingfei Liu
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Mian Faisal Nazir
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China
| | - Shoupu He
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China
| | - Hongge Li
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhaoe Pan
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Panhong Dai
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Liyuan Wang
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Xiongming Du
- Institute of Cotton Research, State Key Laboratory of Cotton Biology, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, Hainan, China.
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14
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Niu H, Ge Q, Shang H, Yuan Y. Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton. Front Genet 2022; 13:855574. [PMID: 35450216 PMCID: PMC9016478 DOI: 10.3389/fgene.2022.855574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
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Gao Y, Chen Y, Song Z, Zhang J, Lv W, Zhao H, Huo X, Zheng L, Wang F, Zhang J, Zhang T. Comparative Dynamic Transcriptome Reveals the Delayed Secondary-Cell-Wall Thickening Results in Altered Lint Percentage and Fiber Elongation in a Chromosomal Segment Substitution Line of Cotton ( Gossypium hirsutum L.). Front Plant Sci 2021; 12:756434. [PMID: 34759948 PMCID: PMC8573213 DOI: 10.3389/fpls.2021.756434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
Lint percentage (LP) is an important yield component in cotton that is usually affected by initial fiber number and cell wall thickness. To explore how fiber cell wall development affects LP, phenotypic identification and dynamic transcriptome analysis were conducted using a single segment substitution line of chromosome 15 (SL15) that harbors a major quantitative trait locus (QTL) for LP. Compared to its recurrent parent LMY22, SL15 did not differ in initial fiber number, but the fiber cell wall thickness and single-fiber weight decreased significantly, altering LP. The comparative transcriptome profiles revealed that the secondary cell wall (SCW) development phase of SL15 was relatively delayed. Meanwhile, the expression of genes related to cell expansion decreased more slightly in SL15 with fiber development, resulting in relatively higher expression at SL15_25D than at LMY22_25D. SCW development-related genes, such as GhNACs and GhMYBs, in the putative NAC-MYB-CESA network differentially expressed at SL15_25D, along with the lower expression of CESA6, CSLC12, and CSLA2. The substituted chromosomal interval was further investigated, and found 6 of 146 candidate genes were differentially expressed in all four cell development periods including 10, 15, 20 and 25 DPA. Genetic variation and co-expression analysis showed that GH_D01G0052, GH_D01G0099, GH_D01G0100, and GH_D01G0140 may be important candidate genes associated with qLP-C15-1. Our results provide novel insights into cell wall development and its relationship with LP, which is beneficial for lint yield and fiber quality improvement.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wanyu Lv
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Han Zhao
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Xuehan Huo
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Ling Zheng
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang-Huai-Hai Plain, Ministry of Agriculture and Rural Affairs, Cotton Research Center, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Life Sciences, Shandong Normal University, Jinan, China
| | - Tianzhen Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, College of Agriculture and Biotechnology, Plant Precision Breeding Academy, Zhejiang University, Hangzhou, China
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16
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Chen J, Zhang H, Dai D, Li X, Ma L, Liang C, Zhang R, Liang C, Du H, Chen Z, Zhao Y, Deng S. A backbone parent contributes key genomic architecture to pedigree breeding of early-season indica rice. J Genet Genomics 2021; 48:1040-1043. [PMID: 34365020 DOI: 10.1016/j.jgg.2021.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 07/13/2021] [Accepted: 07/18/2021] [Indexed: 11/17/2022]
Affiliation(s)
- Junyu Chen
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Huali Zhang
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Dongqing Dai
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Ximing Li
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China
| | - Liangyong Ma
- State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, 310006, China.
| | - Chengzhen Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Rui Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Chengzhi Liang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Huilong Du
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhuo Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yuhui Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Shuhan Deng
- Novogene Bioinformatics Institute, Beijing, 100083, China
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