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Htwe YM, Shi P, Zhang D, Li Z, Yu Q, Wang Y. GWAS determined genetic loci associated with callus induction in oil palm tissue culture. PLANT CELL REPORTS 2024; 43:128. [PMID: 38652306 DOI: 10.1007/s00299-024-03221-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/14/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE GWAS identified six loci at 25 kb downstream of WAK2, a crucial gene for cell wall and callus formation, enabling development of a SNP marker for enhanced callus induction potential. Efficient callus induction is vital for successful oil palm tissue culture, yet identifying genomic loci and markers for early detection of genotypes with high potential of callus induction remains unclear. In this study, immature male inflorescences from 198 oil palm accessions (dura, tenera and pisifera) were used as explants for tissue culture. Callus induction rates were collected at one-, two- and three-months after inoculation (C1, C2 and C3) as phenotypes. Resequencing generated 11,475,258 high quality single nucleotide polymorphisms (SNPs) as genotypes. GWAS was then performed, and correlation analysis revealed a positive association of C1 with both C2 (R = 0.81) and C3 (R = 0.50), indicating that C1 could be used as the major phenotype for callus induction rate. Therefore, only significant SNPs (P ≤ 0.05) in C1 were identified to develop markers for screening individuals with high potential of callus induction. Among 21 significant SNPs in C1, LD block analysis revealed six SNPs on chromosome 12 (Chr12) potentially linked to callus formation. Subsequently, 13 SNP markers were identified from these loci and electrophoresis results showed that marker C-12 at locus Chr12_12704856 can be used effectively to distinguish the GG allele, which showed the highest probability (69%) of callus induction. Furthermore, a rapid SNP variant detection method without electrophoresis was established via qPCR-based melting curve analysis. Our findings facilitated marker-assisted selection for specific palms with high potential of callus induction using immature male inflorescence as explant, aiding ortet palm selection in oil palm tissue culture.
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Affiliation(s)
- Yin Min Htwe
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Peng Shi
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Dapeng Zhang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Zhiying Li
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Qun Yu
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
| | - Yong Wang
- National Key Laboratory for Tropical Crop Breeding, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China.
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Hu D, Zhao Z, Nazir MF, Sun G, Peng Z, Jia Y, Geng X, Wang L, Pan Z, Li H, Chen B, Sun F, He S, Du X. Identification and characterization of candidate genes for primary root length in Asiatic cotton (Gossypium arboreum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:52. [PMID: 38369650 DOI: 10.1007/s00122-023-04471-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/25/2023] [Indexed: 02/20/2024]
Abstract
KEY MESSAGE One major gene controlling primary root length (PRL) in Gossypium arboreum is identified and this research provides a theoretical basis for root development for cotton. Primary root elongation is an essential process in plant root system structure. Here, we investigated the primary root length (PRL) of 215 diploid cotton (G. arboreum) accessions at 5, 8, 10, 15 days after sowing. A Genome-wide association study was performed for the PRL, resulting in 49 significant SNPs associated with 32 putative candidate genes. The SNP with the strongest signal (Chr07_8047530) could clearly distinguish the PRLs between accessions with two haplotypes. GamurG is the only gene that showed higher relative expression in the long PRL genotypes than the short PRL genotypes, which indicated it was the most likely candidate gene for regulating PRL. Moreover, the GamurG-silenced cotton seedlings showed a shorter PRL, while the GamurG-overexpressed Arabidopsis exhibited a significantly longer PRL. Our findings provide insight into the regulation mechanism of cotton root growth and will facilitate future breeding programs to optimize the root system structure in cotton.
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Affiliation(s)
- Daowu Hu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Zibo Zhao
- School of Agriculture Sciences, Zhengzhou University, Zhengzhou, Henan, 450000, China
| | - Mian Faisal Nazir
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
| | - Gaofei Sun
- Anyang Institute of Technology, Anyang, 455000, China
| | - Zhen Peng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Yinhua Jia
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
| | - Xiaoli Geng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
| | - Liru Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
| | - Zhaoe Pan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
| | - Hongge Li
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
| | - Baojun Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
| | - Fenglei Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China
| | - Shoupu He
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
| | - Xiongming Du
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/National Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, Anyang Henan, 455000, China.
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China.
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan, 572024, China.
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Yasir M, Kanwal HH, Hussain Q, Riaz MW, Sajjad M, Rong J, Jiang Y. Status and prospects of genome-wide association studies in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1019347. [PMID: 36330239 PMCID: PMC9623101 DOI: 10.3389/fpls.2022.1019347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
Over the last two decades, the use of high-density SNP arrays and DNA sequencing have allowed scientists to uncover the majority of the genotypic space for various crops, including cotton. Genome-wide association study (GWAS) links the dots between a phenotype and its underlying genetics across the genomes of populations. It was first developed and applied in the field of human disease genetics. Many areas of crop research have incorporated GWAS in plants and considerable literature has been published in the recent decade. Here we will provide a comprehensive review of GWAS studies in cotton crop, which includes case studies on biotic resistance, abiotic tolerance, fiber yield and quality traits, current status, prospects, bottlenecks of GWAS and finally, thought-provoking question. This review will serve as a catalog of GWAS in cotton and suggest new frontiers of the cotton crop to be studied with this important tool.
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Affiliation(s)
- Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Hafiza Hamrah Kanwal
- School of Computer Science, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Quaid Hussain
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Waheed Riaz
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Muhammad Sajjad
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
| | - Yurong Jiang
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou, China
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Cui Z, Liu S, Ge C, Shen Q, Zhang S, Ma H, Liu R, Zhao X, Liu R, Li P, Wang H, Wu Q, Pang C, Chen J. Genome-wide association study reveals that GhTRL1 and GhPIN8 affect cotton root development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3161-3176. [PMID: 35965278 DOI: 10.1007/s00122-022-04177-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Two regions located at chromosome A05 and D04 were found to be significantly associated with 0-0.5 mm and 0.5-2 mm diameter roots, respectively, and two candidate genes related to root development were identified. Roots absorb water and nutrients, and play an important role in plant growth. However, there are few genetic developmental studies on cotton root structural traits. In this study, we used 200 upland cotton (Gossypium hirsutum L.) varieties to analyze the phenotypic variation of 43 traits. A total of 2001 related single-nucleotide polymorphism (SNP) sites located within or near 1046 genes were detected through a genome-wide association study (GWAS). The 32 root traits were linked to SNPs that corresponded to 317 nonrepetitive genes. For SNPs associated with root length and 0-0.5 mm diameter root traits, a significant peak appeared on chromosome A05 (between 21.91 and 22.24 Mb). For SNPs associated with root surface area, root volume and 0.5-2 mm diameter root traits, a significant peak appeared on chromosome D04 (between 7.35 and 7.70 Mb). Within these two key regions, SNPs were detected in the promoter and coding regions of two candidate genes, GhTRL1-A05 and GhPIN8-D04. The expression levels of these two genes also changed significantly according to transcriptome sequencing and quantitative real-time PCR (qRT-PCR). After silencing the GhTRL1 and GhPIN8 genes via virus-induced gene silencing (VIGS), we found that the plants expressing TRV2::GhTRL1 and TRV2::GhPIN8 had a reduced root length, surface area. Moreover, the contents of cis-12-oxo-phytodienoic acid (cis-OPDA), isopentenyl adenosine (iPR) and cis-zeatin (cZ) in the roots of the plants expressing TRV2::GhTRL1 decreased. This study contributes to the cultivation and improvement of cotton varieties.
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Affiliation(s)
- Ziqian Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Shaodong Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Changwei Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Qian Shen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Siping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Huijuan Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruihua Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xinhua Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruida Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Pengzhen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Hongchen Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Qidi Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China.
| | - Jing Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
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Integrating Genome-wide association and whole transcriptome analysis to reveal genetic control of leaf traits in Gossypium arboreum L. Genomics 2022; 114:110331. [PMID: 35278614 DOI: 10.1016/j.ygeno.2022.110331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 02/14/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
Abstract
Leaves are important organs for crop photosynthesis and transpiration, and their morphological characteristics can directly reflect the growth state of plants. Accurate measurement of leaf traits and mining molecular markers are of great significance to the study of cotton growth. Here, we performed a Genome-wide association study on 7 leaf traits in 213 Asian cotton accessions. 32 significant SNPs and 44 genes were identified. A field experiment showed significant difference in leaf hair and leaf area between DPL971 and its natural mutant DPL972. We also compared the leaf transcriptome difference between DPL971 and DPL972, and found a batch of differentially expressed genes and non-coding RNAs (including lncRNAs, microRNAs, and circRNAs). After integrating the GWAS and transcriptome results, we finally selected two coding genes (Ga03G2383 and Ga05G3412) and two microRNAs (hbr-miR156, unconservative_Chr03_contig343_2364) as the candidate for leaf traits. Those findings will provide important genomic resources for cotton leaf improvement breeding.
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