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Gu Q, Lv X, Zhang D, Zhang Y, Wang X, Ke H, Yang J, Chen B, Wu L, Zhang G, Wang X, Sun Z, Ma Z. Deepening genomic sequences of 1081 Gossypium hirsutum accessions reveals novel SNPs and haplotypes relevant for practical breeding utility. Genomics 2024; 116:110848. [PMID: 38663523 DOI: 10.1016/j.ygeno.2024.110848] [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: 01/27/2024] [Revised: 04/16/2024] [Accepted: 04/21/2024] [Indexed: 06/03/2024]
Abstract
Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090, GhM_D05G1692, GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.
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Affiliation(s)
- Qishen Gu
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Xing Lv
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Dongmei Zhang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Yan Zhang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Xingyi Wang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Huifeng Ke
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Jun Yang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Bin Chen
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Liqiang Wu
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Guiyin Zhang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Xingfen Wang
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China
| | - Zhengwen Sun
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, China.
| | - Zhiying Ma
- State Key Laboratory of North China Crop Improvement and Regulation / North China Key Laboratory for Crop Germplasm Resources of Education Ministry / Key Laboratory for Crop Germplasm Resources of Hebei Province / Hebei Agricultural University, Baoding, 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 BIOLOGY 2023; 23:179. [PMID: 37020180 PMCID: PMC10074700 DOI: 10.1186/s12870-023-04147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Upland cotton (Gossypium hirsutum L.) is the most economically important species in the cotton genus (Gossypium spp.). Enhancing the cotton yield is a major goal in cotton breeding programs. Lint percentage (LP) and boll weight (BW) are the two most important components of cotton lint yield. The identification of stable and effective quantitative trait loci (QTLs) will aid the molecular breeding of cotton cultivars with high yield. RESULTS Genotyping by target sequencing (GBTS) and genome-wide association study (GWAS) with 3VmrMLM were used to identify LP and BW related QTLs from two recombinant inbred line (RIL) populations derived from high lint yield and fiber quality lines (ZR014121, CCRI60 and EZ60). The average call rate of a single locus was 94.35%, and the average call rate of an individual was 92.10% in GBTS. A total of 100 QTLs were identified; 22 of them were overlapping with the reported QTLs, and 78 were novel QTLs. Of the 100 QTLs, 51 QTLs were for LP, and they explained 0.29-9.96% of the phenotypic variation; 49 QTLs were for BW, and they explained 0.41-6.31% of the phenotypic variation. One QTL (qBW-E-A10-1, qBW-C-A10-1) was identified in both populations. Six key QTLs were identified in multiple-environments; three were for LP, and three were for BW. A total of 108 candidate genes were identified in the regions of the six key QTLs. Several candidate genes were positively related to the developments of LP and BW, such as genes involved in gene transcription, protein synthesis, calcium signaling, carbon metabolism, and biosynthesis of secondary metabolites. Seven major candidate genes were predicted to form a co-expression network. Six significantly highly expressed candidate genes of the six QTLs after anthesis were the key genes regulating LP and BW and affecting cotton yield formation. CONCLUSIONS A total of 100 stable QTLs for LP and BW in upland cotton were identified in this study; these QTLs could be used in cotton molecular breeding programs. Putative candidate genes of the six key QTLs were identified; this result provided clues for future studies on the mechanisms of LP and BW developments.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Meng Kuang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Longyu Huang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China.
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Institute of Cotton Research, The Ministry of Agriculture, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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Wang C, Liu J, Xie X, Wang J, Ma Q, Chen P, Yang D, Ma X, Hao F, Su J. GhAP1-D3 positively regulates flowering time and early maturity with no yield and fiber quality penalties in upland cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:985-1002. [PMID: 36398758 DOI: 10.1111/jipb.13409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 11/11/2022] [Indexed: 06/16/2023]
Abstract
Flowering time (FTi) is a major factor determining how quickly cotton plants reach maturity. Early maturity greatly affects lint yield and fiber quality and is crucial for mechanical harvesting of cotton in northwestern China. Yet, few quantitative trait loci (QTLs) or genes regulating early maturity have been reported in cotton, and the underlying regulatory mechanisms are largely unknown. In this study, we characterized 152, 68, and 101 loci that were significantly associated with the three key early maturity traits-FTi, flower and boll period (FBP) and whole growth period (WGP), respectively, via four genome-wide association study methods in upland cotton (Gossypium hirsutum). We focused on one major early maturity-related genomic region containing three single nucleotide polymorphisms on chromosome D03, and determined that GhAP1-D3, a gene homologous to Arabidopsis thaliana APETALA1 (AP1), is the causal locus in this region. Transgenic plants overexpressing GhAP1-D3 showed significantly early flowering and early maturity without penalties for yield and fiber quality compared to wild-type (WT) plants. By contrast, the mutant lines of GhAP1-D3 generated by genome editing displayed markedly later flowering than the WT. GhAP1-D3 interacted with GhSOC1 (SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1), a pivotal regulator of FTi, both in vitro and in vivo. Changes in GhAP1-D3 transcript levels clearly affected the expression of multiple key flowering regulatory genes. Additionally, DNA hypomethylation and high levels of H3K9ac affected strong expression of GhAP1-D3 in early-maturing cotton cultivars. We propose that epigenetic modifications modulate GhAP1-D3 expression to positively regulate FTi in cotton through interaction of the encoded GhAP1 with GhSOC1 and affecting the transcription of multiple flowering-related genes. These findings may also lay a foundation for breeding early-maturing cotton varieties in the future.
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Affiliation(s)
- Caixiang Wang
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Juanjuan Liu
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiaoyu Xie
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Ji Wang
- State Key Laboratory of Cotton Biology, College of Life Science, Henan University, Kaifeng, 475004, China
| | - Qi Ma
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Pengyun Chen
- State Key Laboratory of Cotton Biology, College of Life Science, Henan University, Kaifeng, 475004, China
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fushun Hao
- State Key Laboratory of Cotton Biology, College of Life Science, Henan University, Kaifeng, 475004, China
| | - Junji Su
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
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Zhao H, Chen Y, Liu J, Wang Z, Li F, Ge X. Recent advances and future perspectives in early-maturing cotton research. THE NEW PHYTOLOGIST 2023; 237:1100-1114. [PMID: 36352520 DOI: 10.1111/nph.18611] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Cotton's fundamental requirements for long periods of growth and specific seasonal temperatures limit the global arable areas that can be utilized to cultivate cotton. This constraint can be alleviated by breeding for early-maturing varieties. By delaying the sowing dates without impacting the boll-opening time, early-maturing varieties not only mitigate the yield losses brought on by unfavorable weathers in early spring and late autumn but also help reducing the competition between cotton and other crops for arable land, thereby optimizing the cropping system. This review presents studies and breeding efforts for early-maturing cotton, which efficiently pyramid early maturity, high-quality, multiresistance traits, and suitable plant architecture by leveraging pleiotropic genes. Attempts are also made to summarize our current understanding of the molecular mechanisms underlying early maturation, which involves many pathways such as epigenetic, circadian clock, and hormone signaling pathways. Moreover, new avenues and effective measures are proposed for fine-scale breeding of early-maturing crops to ensure the healthy development of the agricultural industry.
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Affiliation(s)
- Hang Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- College of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Yanli Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572000, Hainan, China
| | - Zhi Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Sanya Institute, Zhengzhou University, Sanya, 572000, Hainan, China
| | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Hainan Yazhou Bay Seed Lab, Sanya, 572000, Hainan, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
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Yang P, Sun X, Liu X, Wang W, Hao Y, Chen L, Liu J, He H, Zhang T, Bao W, Tang Y, He X, Ji M, Guo K, Liu D, Teng Z, Liu D, Zhang J, Zhang Z. Identification of Candidate Genes for Lint Percentage and Fiber Quality Through QTL Mapping and Transcriptome Analysis in an Allotetraploid Interspecific Cotton CSSLs Population. FRONTIERS IN PLANT SCIENCE 2022; 13:882051. [PMID: 35574150 PMCID: PMC9100888 DOI: 10.3389/fpls.2022.882051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/06/2022] [Indexed: 06/15/2023]
Abstract
Upland cotton (Gossypium hirsutum) has long been an important fiber crop, but the narrow genetic diversity of modern G. hirsutum limits the potential for simultaneous improvement of yield and fiber quality. It is an effective approach to broaden the genetic base of G. hirsutum through introgression of novel alleles from G. barbadense with excellent fiber quality. In the present study, an interspecific chromosome segment substitution lines (CSSLs) population was established using G. barbadense cultivar Pima S-7 as the donor parent and G. hirsutum cultivar CCRI35 as the recipient parent. A total of 105 quantitative trait loci (QTL), including 85 QTL for fiber quality and 20 QTL for lint percentage (LP), were identified based on phenotypic data collected from four environments. Among these QTL, 25 stable QTL were detected in two or more environments, including four for LP, eleven for fiber length (FL), three for fiber strength (FS), six for fiber micronaire (FM), and one for fiber elongation (FE). Eleven QTL clusters were observed on nine chromosomes, of which seven QTL clusters harbored stable QTL. Moreover, eleven major QTL for fiber quality were verified through analysis of introgressed segments of the eight superior lines with the best comprehensive phenotypes. A total of 586 putative candidate genes were identified for 25 stable QTL associated with lint percentage and fiber quality through transcriptome analysis. Furthermore, three candidate genes for FL, GH_A08G1681 (GhSCPL40), GH_A12G2328 (GhPBL19), and GH_D02G0370 (GhHSP22.7), and one candidate gene for FM, GH_D05G1346 (GhAPG), were identified through RNA-Seq and qRT-PCR analysis. These results lay the foundation for understanding the molecular regulatory mechanism of fiber development and provide valuable information for marker-assisted selection (MAS) in cotton breeding.
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6
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Casale F, Van Inghelandt D, Weisweiler M, Li J, Stich B. Genomic prediction of the recombination rate variation in barley - A route to highly recombinogenic genotypes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:676-690. [PMID: 34783155 PMCID: PMC8989500 DOI: 10.1111/pbi.13746] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/06/2021] [Accepted: 11/07/2021] [Indexed: 06/13/2023]
Abstract
Meiotic recombination is not only fundamental to the adaptation of sexually reproducing eukaryotes in nature but increased recombination rates facilitate the combination of favourable alleles into a single haplotype in breeding programmes. The main objectives of this study were to (i) assess the extent and distribution of the recombination rate variation in cultivated barley (Hordeum vulgare L.), (ii) quantify the importance of the general and specific recombination effects, and (iii) evaluate a genomic selection approach's ability to predict the recombination rate variation. Genetic maps were created for the 45 segregating populations that were derived from crosses among 23 spring barley inbreds with origins across the world. The genome-wide recombination rate among populations ranged from 0.31 to 0.73 cM/Mbp. The crossing design used in this study allowed to separate the general recombination effects (GRE) of individual parental inbreds from the specific recombination effects (SRE) caused by the combinations of parental inbreds. The variance of the genome-wide GRE was found to be about eight times the variance of the SRE. This finding indicated that parental inbreds differ in the efficiency of their recombination machinery. The ability to predict the chromosome or genome-wide recombination rate of an inbred ranged from 0.80 to 0.85. These results suggest that a reliable screening of large genetic materials for their potential to cause a high extent of genetic recombination in their progeny is possible, allowing to systematically manipulate the recombination rate using natural variation.
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Affiliation(s)
- Federico Casale
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Delphine Van Inghelandt
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Marius Weisweiler
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
| | - Jinquan Li
- Max Planck Institute for Plant Breeding ResearchKölnGermany
- Strube D&S GmbHSöllingenGermany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of PlantsHeinrich Heine UniversityDüsseldorfGermany
- Max Planck Institute for Plant Breeding ResearchKölnGermany
- Cluster of Excellence on Plant SciencesFrom Complex Traits Towards Synthetic ModulesDüsseldorfGermany
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7
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Niu H, Ge Q, Shang H, Yuan Y. Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton. Front Genet 2022; 13:855574. [PMID: 35450216 PMCID: PMC9016478 DOI: 10.3389/fgene.2022.855574] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
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Zhang J, Guan X, Lu Y, Liu Y, Xu N, Cai C, Li Q, Liu J, Wang Y, Liu J. Titanium dioxide-mediated fatty acids promoted carotenoid synthesis in Phaffia rhodozyma PR106 analyzed whole genome. BIORESOURCE TECHNOLOGY 2022; 347:126699. [PMID: 35017091 DOI: 10.1016/j.biortech.2022.126699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/05/2022] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Carotenoid, as good colorant and antioxidant, is widely used in the fields of food, medicine and feed. The whole genome of P. rhodozyma PR106 strain with 228.77 mg/L carotenoid (mainly included astaxanthin, β-carotene and lycopene) yield was sequenced, and the genome size was 16.18 Mb, the GC content was 47%. The genetic evolution analysis indicated that PR106 greatly changed in evolution process, and closely related to P. rhodozyma CBS7918. Under 500 mg/L titanium dioxide (TiO2) stress, carotenoid yield of PR106 was 2.15 times that of the control for 48 h, and was 305.12 mg/L in PR106 to 72 h, interestingly, the yield of oleate, linoleate and α-linolenate also increased significantly among 51 fatty acids by targeted metabolomics analysis. TiO2 promoted carotenoid synthesis of PR106 by forming astaxanthin esters to reduce the feedback inhibition of carotenoid synthesis. These results provided a theoretical basis for carotenoid production and development using P. rhodozyma.
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Affiliation(s)
- Jing Zhang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Xiaoyu Guan
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Yanhong Lu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Yankai Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Na Xu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Chunyu Cai
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Qingru Li
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Jiahuan Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China
| | - Yuhua Wang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China; National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China.
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, China; Jilin Province Innovation Center for Food Biological Manufacture, Jilin Agricultural University, Changchun, China; National Engineering Laboratory for Wheat and Corn Deep Processing, Changchun, China
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9
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Liu X, Yang L, Wang J, Wang Y, Guo Z, Li Q, Yang J, Wu Y, Chen L, Teng Z, Liu D, Liu D, Guo K, Zhang Z. Analyzing Quantitative Trait Loci for Fiber Quality and Yield-Related Traits From a Recombinant Inbred Line Population With Gossypium hirsutum Race palmeri as One Parent. FRONTIERS IN PLANT SCIENCE 2022; 12:817748. [PMID: 35046989 PMCID: PMC8763314 DOI: 10.3389/fpls.2021.817748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Fiber quality and yield-related traits are important agronomic traits in cotton breeding. To detect the genetic basis of fiber quality and yield related traits, a recombinant inbred line (RIL) population consisting of 182 lines was established from a cross between Gossypium hirsutum cultivar CCRI35 and G. hirsutum race palmeri accession TX-832. The RIL population was deeply genotyped using SLAF-seq and was phenotyped in six environments. A high-density genetic linkage map with 15,765 SNP markers and 153 SSR markers was constructed, with an average distance of 0.30 cM between adjacent markers. A total of 210 fiber quality quantitative trait loci (QTLs) and 73 yield-related QTLs were identified. Of the detected QTLs, 62 fiber quality QTLs and 10 yield-related QTLs were stable across multiple environments. Twelve and twenty QTL clusters were detected on the At and Dt subgenome, respectively. Twenty-three major QTL clusters were further validated through associated analysis and five candidate genes of four stable fiber quality QTLs were identified. This study revealed elite loci influencing fiber quality and yield and significant phenotypic selection regions during G. hirsutum domestication, and set a stage for future utilization of molecular marker assisted breeding in cotton breeding programs.
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Feng L, Chen Y, Xu M, Yang Y, Yue H, Su Q, Zhou C, Feng G, Ai N, Wang N, Zhou B. Genome-Wide Introgression and Quantitative Trait Locus Mapping Reveals the Potential of Asian Cotton ( Gossypium arboreum) in Improving Upland Cotton ( Gossypium hirsutum). FRONTIERS IN PLANT SCIENCE 2021; 12:719371. [PMID: 34408767 PMCID: PMC8365338 DOI: 10.3389/fpls.2021.719371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
Gossypium arboreum (2n=2x=26, A2), the putative progenitor of the At-subgenome of Gossypium hirsutum (2n=4x=52, AD), is a repository of genes of interesting that have been eliminated during evolution/domestication of G. hirsutum. However, its valuable genes remain untapped so far due to species isolation. Here, using a synthetic amphiploid (AADDA2A2) previously reported, we developed a set of 289 G. arboreum chromosome segment introgression lines (ILs) in G. hirsutum by expanding the backcrossing population and through precise marker-assisted selection (MAS) although complex chromosomal structural variations existed between parents which severely hindered introgression. Our results showed the total coverage length of introgressed segments was 1,116.29 Mb, representing 78.48% of the At-subgenome in the G. hirsutum background, with an average segment-length of 8.69 Mb. A total of 81 co- quantitative trait loci (QTLs) for yield and fiber quality were identified by both the RSTEP-ADD-based QTL mapping and the genome-wide association study (GWAS) analysis, with 1.01-24.78% of the phenotypic variance explained. Most QTLs for boll traits showed negative additive effects, but G. arboreum still has the potential to improve boll-number traits in G. hirsutum. Most QTLs for fiber quality showed negative additive effects, implying these QTLs were domesticated in G. hirsutum compared with G. arboreum and, a small quantity of fiber quality QTLs showing positive additive effects, conversely; however, indicates that G. arboreum has the underlying genes of enhancing fiber quality of G. hirsutum. This study provides new insights into the breeding genetic potential of G. arboreum, lays the foundation for further mining favorable genes of interest, and provides guidance for inter-ploidy gene transference from relatives into cultivated crops.
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Affiliation(s)
- Liuchun Feng
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Yu Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Min Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Ying Yang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Haoran Yue
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Qiao Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Chenhui Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Guoli Feng
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Nijiang Ai
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Ningshan Wang
- Shihezi Agricultural Science Research Institute, Shihezi, China
| | - Baoliang Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
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Ma Y, Min L, Wang J, Li Y, Wu Y, Hu Q, Ding Y, Wang M, Liang Y, Gong Z, Xie S, Su X, Wang C, Zhao Y, Fang Q, Li Y, Chi H, Chen M, Khan AH, Lindsey K, Zhu L, Li X, Zhang X. A combination of genome-wide and transcriptome-wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton. THE NEW PHYTOLOGIST 2021; 231:165-181. [PMID: 33665819 PMCID: PMC8252431 DOI: 10.1111/nph.17325] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 02/23/2021] [Indexed: 05/23/2023]
Abstract
Global warming has reduced the productivity of many field-grown crops, as the effects of high temperatures can lead to male sterility in such plants. Genetic regulation of the high temperature (HT) response in the major crop cotton is poorly understood. We determined the functionality and transcriptomes of the anthers of 218 cotton accessions grown under HT stress. By analyzing transcriptome divergence and implementing a genome-wide association study (GWAS), we identified three thermal tolerance associated loci which contained 75 protein coding genes and 27 long noncoding RNAs, and provided expression quantitative trait loci (eQTLs) for 13 132 transcripts. A transcriptome-wide association study (TWAS) confirmed six causal elements for the HT response (three genes overlapped with the GWAS results) which are involved in protein kinase activity. The most susceptible gene, GhHRK1, was confirmed to be a previously uncharacterized negative regulator of the HT response in both cotton and Arabidopsis. These functional variants provide a new understanding of the genetic basis for HT tolerance in male reproductive organs.
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Affiliation(s)
- Yizan Ma
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Ling Min
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Junduo Wang
- Xinjiang Academy of Agricultural ScienceXinjiang830000China
| | - Yaoyao Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yuanlong Wu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Qin Hu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yuanhao Ding
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yajun Liang
- Xinjiang Academy of Agricultural ScienceXinjiang830000China
| | - Zhaolong Gong
- Xinjiang Academy of Agricultural ScienceXinjiang830000China
| | - Sai Xie
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Xiaojun Su
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Chaozhi Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yunlong Zhao
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Qidi Fang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Yanlong Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Huabin Chi
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Miao Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Aamir Hamid Khan
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Keith Lindsey
- Department of BiosciencesDurham UniversityDurhamDH1 3LEUK
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
| | - Xueyuan Li
- Xinjiang Academy of Agricultural ScienceXinjiang830000China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhan430070China
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Yuan D, Grover CE, Hu G, Pan M, Miller ER, Conover JL, Hunt SP, Udall JA, Wendel JF. Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2003634. [PMID: 34026441 PMCID: PMC8132148 DOI: 10.1002/advs.202003634] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 02/02/2021] [Indexed: 05/09/2023]
Abstract
The two cultivated allopolyploid cottons, Gossypium hirsutum and Gossypium barbadense, represent a remarkable example of parallel independent domestication, both involving dramatic morphological transformations under selection from wild perennial plants to annualized row crops. Deep resequencing of 643 newly sampled accessions spanning the wild-to-domesticated continuum of both species, and their allopolyploid relatives, are combined with existing data to resolve species relationships and elucidate multiple aspects of their parallel domestication. It is confirmed that wild G. hirsutum and G. barbadense were initially domesticated in the Yucatan Peninsula and NW South America, respectively, and subsequently spread under domestication over 4000-8000 years to encompass most of the American tropics. A robust phylogenomic analysis of infraspecific relationships in each species is presented, quantify genetic diversity in both, and describe genetic bottlenecks associated with domestication and subsequent diffusion. As these species became sympatric over the last several millennia, pervasive genome-wide bidirectional introgression occurred, often with striking asymmetries involving the two co-resident genomes of these allopolyploids. Diversity scans revealed genomic regions and genes unknowingly targeted during domestication and additional subgenomic asymmetries. These analyses provide a comprehensive depiction of the origin, divergence, and adaptation of cotton, and serve as a rich resource for cotton improvement.
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Affiliation(s)
- Daojun Yuan
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
- College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070China
| | - Corrinne E. Grover
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Guanjing Hu
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Mengqiao Pan
- State Key Laboratory of Crop Genetics and Germplasm EnhancementCotton Hybrid R & D Engineering CenterNanjing Agricultural UniversityNanjing210095China
| | - Emma R. Miller
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | - Justin L. Conover
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
| | | | - Joshua A. Udall
- Crop Germplasm Research UnitUSDA‐ARSCollege StationTX77845USA
| | - Jonathan F. Wendel
- Department of EcologyEvolution, and Organismal Biology (EEOB)Bessey HallIowa State UniversityAmesIA50011USA
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Gossypium tomentosum genome and interspecific ultra-dense genetic maps reveal genomic structures, recombination landscape and flowering depression in cotton. Genomics 2021; 113:1999-2009. [PMID: 33915244 DOI: 10.1016/j.ygeno.2021.04.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/08/2021] [Accepted: 04/24/2021] [Indexed: 11/21/2022]
Abstract
The high-quality reference-grade genome for Gossupium tomentosum can greatly promote the progress in biological research and introgression breeding for the mainly cultivated species, G. hirsutum. Here, we report a high-quality genome assembly for G. tomentosum by integrating PacBio and Hi-C technologies. Comparative genomic analysis revealed a large number of genetic variations. Two re-sequencing-based ultra-dense genetic maps were constructed which comprised 4,047,199 and 6,009,681 SNPs, 4120 and 4599 bins and covering 4126.36 cM and 4966.72 cM in the EMF2 (F2 from G. hirsutum × G. tomentosum) and GHF2 (F2 from G. hirsutum × G. barbadense). The EMF2 exhibited lower recombination rate at the whole-genome level as compared with GHF2. We mapped 22 and 33 QTL associated with crossover frequency and predicted Gh_MRE11 and Gh_FIGL1 as the candidate genes governing crossover in the EMF2 and GHF2, respectively. We identified 13 significant QTL that regulate the floral transition, and revealed that Gh_AGL18 was associated with the floral transition. Therefore, our study provides a valuable genomic resource to support a better understanding of cotton interspecific cross and recombination landscape for genetic improvement and breeding in cotton.
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14
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Lian Q, Fu Q, Xu Y, Hu Z, Zheng J, Zhang A, He Y, Wang C, Xu C, Chen B, Garcia-Mas J, Zhao G, Wang H. QTLs and candidate genes analyses for fruit size under domestication and differentiation in melon (Cucumis melo L.) based on high resolution maps. BMC PLANT BIOLOGY 2021; 21:126. [PMID: 33658004 PMCID: PMC7931605 DOI: 10.1186/s12870-021-02904-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/24/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Melon is a very important horticultural crop produced worldwide with high phenotypic diversity. Fruit size is among the most important domestication and differentiation traits in melon. The molecular mechanisms of fruit size in melon are largely unknown. RESULTS Two high-density genetic maps were constructed by whole-genome resequencing with two F2 segregating populations (WAP and MAP) derived from two crosses (cultivated agrestis × wild agrestis and cultivated melo × cultivated agrestis). We obtained 1,871,671 and 1,976,589 high quality SNPs that show differences between parents in WAP and MAP. A total of 5138 and 5839 recombination events generated 954 bins in WAP and 1027 bins in MAP with the average size of 321.3 Kb and 301.4 Kb respectively. All bins were mapped onto 12 linkage groups in WAP and MAP. The total lengths of two linkage maps were 904.4 cM (WAP) and 874.5 cM (MAP), covering 86.6% and 87.4% of the melon genome. Two loci for fruit size were identified on chromosome 11 in WAP and chromosome 5 in MAP, respectively. An auxin response factor and a YABBY transcription factor were inferred to be the candidate genes for both loci. CONCLUSION The high-resolution genetic maps and QTLs analyses for fruit size described here will provide a better understanding the genetic basis of domestication and differentiation, and provide a valuable tool for map-based cloning and molecular marker assisted breeding.
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Affiliation(s)
- Qun Lian
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
| | - Qiushi Fu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yongyang Xu
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Zhicheng Hu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Jing Zheng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Aiai Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China
| | - Yuhua He
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Changsheng Wang
- National Center for Gene Research, CAS Center for Excellence in Molecular Plant Sciences, Shanghai, 200000, China
| | - Chuanqiang Xu
- Shenyang Agricultural University, College of Horticulture, Shenyang, 110866, China
| | - Benxue Chen
- Design Gollege, Zhoukou Normal University, Zhoukou, 466000, China
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Barcelona, Spain
| | - Guangwei Zhao
- Henan Key Laboratory of Fruit and Cucurbit Biology, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China.
| | - Huaisong Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, 100081, Beijing, China.
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15
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Song X, Zhu G, Hou S, Ren Y, Amjid MW, Li W, Guo W. Genome-Wide Association Analysis Reveals Loci and Candidate Genes Involved in Fiber Quality Traits Under Multiple Field Environments in Cotton ( Gossypium hirsutum). FRONTIERS IN PLANT SCIENCE 2021; 12:695503. [PMID: 34421946 PMCID: PMC8374309 DOI: 10.3389/fpls.2021.695503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/16/2021] [Indexed: 05/17/2023]
Abstract
Fiber length, fiber strength, and fiber micronaire are the main fiber quality parameters in cotton. Thus, mining the elite and stable loci/alleles related to fiber quality traits and elucidating the relationship between the two may accelerate genetic improvement of fiber quality in cotton. Here, genome-wide association analysis (GWAS) was performed for fiber quality parameters based on phenotypic data, and 56,010 high-quality single nucleotide polymorphisms (SNPs) using 242 upland cotton accessions under 12 field environments were obtained. Phenotypic analysis exhibited that fiber length (FL) had a positive correlation with fiber strength (FS) and had a negative correlation with fiber micronaire (Mic). Genetic analysis also indicated that FL, FS, and Mic had high heritability of more than 80%. A total of 67 stable quantitative trait loci (QTLs) were identified through GWAS analysis, including 31 for FL, 21 for FS, and 22 for Mic. Of them, three pairs homologous QTLs were detected between A and D subgenomes, and seven co-located QTLs with two fiber quality parameters were found. Compared with the reported QTLs, 34 co-located with previous studies, and 33 were newly revealed. Integrated with transcriptome analysis, we selected 256, 244, and 149 candidate genes for FL, FS, and Mic, respectively. Gene Ontology (GO) analysis showed that most of the genes located in QTLs interval of the three fiber quality traits were involved in sugar biosynthesis, sugar metabolism, microtubule, and cytoskeleton organization, which played crucial roles in fiber development. Through correlation analysis between haplotypes and phenotypes, three genes (GH_A05G1494, GH_D11G3097, and GH_A05G1082) predominately expressed in fiber development stages were indicated to be potentially responsible for FL, FS, and Mic, respectively. The GH_A05G1494 encoded a protein containing SGS-domain, which is related to tubulin-binding and ubiquitin-protein ligase binding. The GH_D11G3097 encoded 20S proteasome beta subunit G1, and was involved in the ubiquitin-dependent protein catabolic process. The GH_A05G1082 encoded RAN binding protein 1 with a molecular function of GTPase activator activity. These results provide new insights and candidate loci/genes for the improvement of fiber quality in cotton.
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Dai P, Sun G, Jia Y, Pan Z, Tian Y, Peng Z, Li H, He S, Du X. Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3273-3285. [PMID: 32844253 DOI: 10.1007/s00122-020-03668-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 08/08/2020] [Indexed: 05/06/2023]
Abstract
Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding.
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Affiliation(s)
- Panhong Dai
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Gaofei Sun
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- School of Computer Science & Information Engineering, Anyang Institute of Technology, Anyang, 455000, China
| | - Yinhua Jia
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhaoe Pan
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yingbing Tian
- Agricultural College, Yangtze University, Jingzhou, 434000, China
| | - Zhen Peng
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongge Li
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China
| | - Shoupu He
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiongming Du
- Research Base, Anyang Institute of Technology, State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, China.
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Su J, Wang C, Ma Q, Zhang A, Shi C, Liu J, Zhang X, Yang D, Ma X. An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton. BMC PLANT BIOLOGY 2020; 20:416. [PMID: 32894064 PMCID: PMC7487830 DOI: 10.1186/s12870-020-02613-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Cotton (Gossypium spp.) fiber yield is one of the key target traits, and improved fiber yield has always been thought of as an important objective in the breeding programs and production. Although some studies had been reported for the understanding of genetic bases for cotton yield-related traits, the detected quantitative trait loci (QTL) for the traits is still very limited. To uncover the whole-genome QTL controlling three yield-related traits in upland cotton (Gossypium hirsutum L.), phenotypic traits were investigated under four planting environments and 9244 single-nucleotide polymorphism linkage disequilibrium block (SNPLDB) markers were developed in an association panel consisting of 315 accessions. RESULTS A total of 53, 70 and 68 significant SNPLDB loci associated with boll number (BN), boll weight (BW) and lint percentage (LP), were respectively detected through a restricted two-stage multi-locus multi-allele genome-wide association study (RTM-GWAS) procedure in multiple environments. The haplotype/allele effects of the significant SNPLDB loci were estimated and the QTL-allele matrices were organized for offering the abbreviated genetic composition of the population. Among the significant SNPLDB loci, six of them were simultaneously identified in two or more single planting environments and were thought of as the stable SNPLDB loci. Additionally, a total of 115 genes were annotated in the nearby regions of the six stable SNPLDB loci, and 16 common potential candidate genes controlling target traits of them were predicted by two RNA-seq data. One of 16 genes (GH_D06G2161) was mainly expressed in the early ovule-development stages, and the stable SNPLDB locus (LDB_19_62926589) was mapped in its promoter region. CONCLUSION This study identified the QTL alleles and candidate genes that could provide important insights into the genetic basis of yield-related traits in upland cotton and might facilitate breeding cotton varieties with high yield.
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Affiliation(s)
- Junji Su
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Caixiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Qi Ma
- Cotton Research Institute, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, China
| | - Ai Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Chunhui Shi
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Juanjuan Liu
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xianliang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Delong Yang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Xiongfeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China.
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18
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Yang Z, Qanmber G, Wang Z, Yang Z, Li F. Gossypium Genomics: Trends, Scope, and Utilization for Cotton Improvement. TRENDS IN PLANT SCIENCE 2020; 25:488-500. [PMID: 31980282 DOI: 10.1016/j.tplants.2019.12.011] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 11/19/2019] [Accepted: 12/09/2019] [Indexed: 05/23/2023]
Abstract
Cotton (Gossypium spp.) is the most important natural fiber crop worldwide. The diversity of Gossypium species also provides an ideal model for investigating evolution and domestication of polyploids. However, the huge and complex cotton genome hinders genomic research. Technical advances in high-throughput sequencing and bioinformatics analysis have now largely overcome these obstacles, bringing about a new era of cotton genomics. Here, we review recent progress in Gossypium genomics based on whole genome sequencing, resequencing, and comparative genomics, which have provided insights about the genomic basis of fiber biogenesis and the landscape of cotton functional genomics. We address current challenges and present multidisciplinary genomics-enabled breeding strategies covering the breadth of high fiber yield, quality, and environmental resilience for future cotton breeding programs.
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Affiliation(s)
- Zuoren Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Ghulam Qanmber
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhi Wang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Zhaoen Yang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
| | - Fuguang Li
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, 450001, Henan, China; State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, Henan, China.
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19
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Long L, Liu J, Gao Y, Xu FC, Zhao JR, Li B, Gao W. Flavonoid accumulation in spontaneous cotton mutant results in red coloration and enhanced disease resistance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 143:40-49. [PMID: 31479881 DOI: 10.1016/j.plaphy.2019.08.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/16/2019] [Accepted: 08/26/2019] [Indexed: 05/07/2023]
Abstract
Cotton, the leading natural fiber, is cultivated worldwide, but its production is seriously threatened by pathogens. Accordingly, the selection of resistant cultivars has become a key priority of cotton breeding programs. In this study, a spontaneous mutant with red coloration (S156) and a control cultivar (S78) were used as experimental materials for a comparative analysis. Metabolomic analysis revealed the enrichment of flavonoids in S156 leaves compared with S78 leaves, and transcriptomic analysis revealed the upregulated expression of flavonoid biosynthesis genes in S156 leaves relative to S78 leaves. In addition, the red mutant showed a significantly increase in resistance to Verticillium dahliae, a fungal pathogen that poses a major threat to cotton production. The pathogen invasion process was suppressed in the red cotton cultivar. This study reveals the mechanism underlying the red coloration of S156 cotton and indicates the great potential of red cotton in pathogen- and insect-resistant breeding of cotton.
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Affiliation(s)
- Lu Long
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan, 475004, PR China.
| | - Ji Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, Henan, 455000, PR China.
| | - Ya Gao
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan, 475004, PR China
| | - Fu-Chun Xu
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan, 475004, PR China
| | - Jing-Ruo Zhao
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan, 475004, PR China
| | - Bing Li
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan, 475004, PR China
| | - Wei Gao
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Science, Henan University, Kaifeng, Henan, 475004, PR China.
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