1
|
Varotto S, Krugman T, Aiese Cigliano R, Kashkush K, Kondić-Špika A, Aravanopoulos FA, Pradillo M, Consiglio F, Aversano R, Pecinka A, Miladinović D. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3987-4003. [PMID: 35678824 PMCID: PMC9729329 DOI: 10.1007/s00122-022-04122-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/04/2022] [Indexed: 05/05/2023]
Abstract
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.
Collapse
Affiliation(s)
- Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment, University of Padova, Viale dell'Università, 16 35020, Legnaro, Italy.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beersheba, 84105, Israel
| | - Ankica Kondić-Špika
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| | - Fillipos A Aravanopoulos
- Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, GR54006, Greece
| | - Monica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040, Madrid, Spain
| | - Federica Consiglio
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Università 133, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Ales Pecinka
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Acad Sci, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| |
Collapse
|
2
|
Quan C, Chen G, Li S, Jia Z, Yu P, Tu J, Shen J, Yi B, Fu T, Dai C, Ma C. Transcriptome shock in interspecific F1 allotriploid hybrids between Brassica species. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:2336-2353. [PMID: 35139197 DOI: 10.1093/jxb/erac047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 02/03/2022] [Indexed: 06/14/2023]
Abstract
Interspecific hybridization drives the evolution of angiosperms and can be used to introduce novel alleles for important traits or to activate heterosis in crop breeding. Hybridization brings together gene expression networks from two different species, potentially causing global alterations of gene expression in the F1 plants which is called 'transcriptome shock'. Here, we explored such a transcriptome shock in allotriploid Brassica hybrids. We generated interspecific F1 allotriploid hybrids between the allotetraploid species Brassica napus and three accessions of the diploid species Brassica rapa. RNA-seq of the F1 hybrids and the parental plants revealed that 26.34-30.89% of genes were differentially expressed between the parents. We also analyzed expression level dominance and homoeolog expression bias between the parents and the F1 hybrids. The expression-level dominance biases of the Ar, An, and Cn subgenomes was genotype and stage dependent, whereas significant homoeolog expression bias was observed among three subgenomes from different parents. Furthermore, more genes were involved in trans regulation than in cis regulation in allotriploid F1 hybrids. Our findings provide new insights into the transcriptomic responses of cross-species hybrids and hybrids showing heterosis, as well as a new method for promoting the breeding of desirable traits in polyploid Brassica species.
Collapse
Affiliation(s)
- Chengtao Quan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Guoting Chen
- College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Sijia Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Pugang Yu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| |
Collapse
|
3
|
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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 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] [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.
Collapse
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.
| |
Collapse
|
4
|
Ding Y, Zhang R, Zhu L, Wang M, Ma Y, Yuan D, Liu N, Hu H, Min L, Zhang X. An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid 'Huaza Mian H318', as revealed by genome-wide gene expression analysis. BMC Genomics 2021; 22:277. [PMID: 33865322 PMCID: PMC8052695 DOI: 10.1186/s12864-021-07580-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 04/04/2021] [Indexed: 12/15/2022] Open
Abstract
Background Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton. Results The elite cotton hybrid variety ‘Huaza Mian H318’ (H318) and its parental lines were used to explore the source of its yield heterosis. A four-year investigation of yield-related traits showed that the boll number of H318 showed higher stability than that of its two parents, both in suitable and unsuitable climate years. In addition, the hybrid H318 grew faster and showed higher fresh and dry weights than its parental lines at the seedling stage. Transcriptome analysis of seedlings identified 17,308 differentially expressed genes (DEGs) between H318 and its parental lines, and 3490 extremely changed DEGs were screened out for later analysis. Most DEGs (3472/3490) were gathered between H318 and its paternal line (4–5), and only 64 DEGs were found between H318 and its maternal line (B0011), which implied that H318 displays more similar transcriptional patterns to its maternal parent at the seedling stage. GO and KEGG analyses showed that these DEGs were highly enriched in photosynthesis, lipid metabolic, carbohydrate metabolic and oxidation-reduction processes, and the expression level of these DEGs was significantly higher in H318 relative to its parental lines, which implied that photosynthesis, metabolism and stress resistances were enhanced in H318. Conclusion The enhanced photosynthesis, lipid and carbohydrate metabolic capabilities contribute to the heterosis of H318 at the seedling stage, and establishes a material foundation for subsequent higher boll-setting rates in complex field environments. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07580-8.
Collapse
Affiliation(s)
- Yuanhao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Rui Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Longfu Zhu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yizan Ma
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Daojun Yuan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyan Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.,Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Ling Min
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| |
Collapse
|
5
|
Shahzad K, Zhang X, Guo L, Qi T, Bao L, Zhang M, Zhang B, Wang H, Tang H, Qiao X, Feng J, Wu J, Xing C. Comparative transcriptome analysis between inbred and hybrids reveals molecular insights into yield heterosis of upland cotton. BMC PLANT BIOLOGY 2020; 20:239. [PMID: 32460693 PMCID: PMC7251818 DOI: 10.1186/s12870-020-02442-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/13/2020] [Indexed: 05/12/2023]
Abstract
BACKGROUND Utilization of heterosis has greatly improved the productivity of many crops worldwide. Understanding the potential molecular mechanism about how hybridization produces superior yield in upland cotton is critical for efficient breeding programs. RESULTS In this study, high, medium, and low hybrids varying in the level of yield heterosis were screened based on field experimentation of different years and locations. Phenotypically, high hybrid produced a mean of 14% more seed cotton yield than its better parent. Whole-genome RNA sequencing of these hybrids and their four inbred parents was performed using different tissues of the squaring stage. Comparative transcriptomic differences in each hybrid parent triad revealed a higher percentage of differentially expressed genes (DEGs) in each tissue. Expression level dominance analysis identified majority of hybrids DEGs were biased towards parent like expressions. An array of DEGs involved in ATP and protein binding, membrane, cell wall, mitochondrion, and protein phosphorylation had more functional annotations in hybrids. Sugar metabolic and plant hormone signal transduction pathways were most enriched in each hybrid. Further, these two pathways had most mapped DEGs on known seed cotton yield QTLs. Integration of transcriptome, QTLs, and gene co-expression network analysis discovered genes Gh_A03G1024, Gh_D08G1440, Gh_A08G2210, Gh_A12G2183, Gh_D07G1312, Gh_D08G1467, Gh_A03G0889, Gh_A08G2199, and Gh_D05G0202 displayed a complex regulatory network of many interconnected genes. qRT-PCR of these DEGs was performed to ensure the accuracy of RNA-Seq data. CONCLUSIONS Through genome-wide comparative transcriptome analysis, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.
Collapse
Affiliation(s)
- Kashif Shahzad
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Xuexian Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Liping Guo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Tingxiang Qi
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Lisheng Bao
- Jinhua Department of Economic Special Technology Promotion, Jinhua, 321017 Zhejiang China
| | - Meng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Bingbing Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Hailin Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Huini Tang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Xiuqin Qiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Juanjuan Feng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Jianyong Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| | - Chaozhu Xing
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Key Laboratory for Cotton Genetic Improvement, Ministry of Agriculture, 38 Huanghe Dadao, Anyang, 455000 Henan China
| |
Collapse
|
6
|
Nadir S, Li W, Zhu Q, Khan S, Zhang XL, Zhang H, Wei ZF, Li MT, Zhou L, Li CY, Chen LJ, Lee DS. A novel discovery of a long terminal repeat retrotransposon-induced hybrid weakness in rice. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:1197-1207. [PMID: 30576523 PMCID: PMC6382335 DOI: 10.1093/jxb/ery442] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 12/04/2018] [Indexed: 06/09/2023]
Abstract
Hybrid weakness is a post-zygotic hybridization barrier frequently observed in plants, including rice. In this study, we describe the genomic variation among three temperate japonica rice (Oryza sativa ssp. japonica) varieties 'Aranghyangchalbyeo' ('CH7'), 'Sanghaehyangheolua' ('CH8') and 'Shinseonchalbyeo' ('CH9'), carrying different hybrid weakness genes. The reciprocal progeny obtained from crossing any two varieties displayed characteristic hybrid weakness traits. We mapped and cloned a new locus, Hwc3 (hybrid weakness 3), on chromosome 4. Sequence analysis identified that a long terminal repeat (LTR) retrotransposon was inserted into the promoter region of the Hwc3 gene in 'CH7'. A 4-kb DNA fragment from 'CH7' containing the Hwc3 gene with the inserted LTR retrotransposon was able to induce hybrid weakness in hybrids with 'CH8' plants carrying the Hwc1 gene by genetic complementation. We investigated the differential gene expression profile of F1 plants exhibiting hybrid weakness and detected that the genes associated with energy metabolism were significantly down-regulated compared with the parents. Based on our results, we propose that LTR retrotransposons could be a potential cause of hybrid weakness in intrasubspecific hybrids in japonica rice. Understanding the molecular mechanisms underlying intrasubspecific hybrid weakness is important for increasing our knowledge on reproductive isolation and could have significant implications for rice improvement and hybrid breeding.
Collapse
Affiliation(s)
- Sadia Nadir
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- Department of Chemistry, University of Science and Technology, Bannu, KPK, Pakistan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wei Li
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Qian Zhu
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Sehroon Khan
- Centre for Mountain Ecosystem Studies, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, China
- World Agroforestry Centre, East and Central Asia, Kunming, Yunnan, China
| | - Xiao-Ling Zhang
- Agricultural College of Kunming University, Kunming, Yunnan, China
| | - Hui Zhang
- College of Agronomy and Biotechnology, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Zhen-Fei Wei
- Maize Research Institute, Shanxi Academy of Agriculture Sciences, Xinzhou, Shanxi, China
| | - Meng-Ting Li
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Li Zhou
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
| | - Cheng-Yun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Li-Juan Chen
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Dong-Sun Lee
- Rice Research Institute, Yunnan Agriculture University, Kunming, Yunnan, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, Yunnan, China
| |
Collapse
|
7
|
Zhao C, Zhao G, Geng Z, Wang Z, Wang K, Liu S, Zhang H, Guo B, Geng J. Physical mapping and candidate gene prediction of fertility restorer gene of cytoplasmic male sterility in cotton. BMC Genomics 2018; 19:6. [PMID: 29295711 PMCID: PMC5751606 DOI: 10.1186/s12864-017-4406-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 12/20/2017] [Indexed: 12/04/2022] Open
Abstract
Background Cytoplasmic male sterility (CMS) is a maternally inherited trait failing to produce functional pollen. It plays a pivotal role in the exploitation of crop heterosis. The specific locus amplified fragment sequencing (SLAF-seq) as a high-resolution strategy for the identification of new SNPs on a large-scale is gradually applied for functional gene mining. The current study combined the bulked segregant analysis (BSA) with SLAF-seq to identify the candidate genes associated with fertility restorer gene (Rf) in CMS cotton. Methods Illumina sequencing systematically investigated the parents. A segregating population comprising of 30 + 30 F2 individuals was developed using 3096A (female parent) as sterile and 866R (male parent) as a restorer. The original data obtained by dual-index sequencing were analyzed to obtain the reads of each sample that were compared to the reference genome in order to identify the SLAF tag with a polymorphism in parent lines and the SNP with read-associated coverage. Based on SLAF tags, SNP-index analysis, Euclidean distance (ED) correlation analysis, and whole genome resequencing, the hot regions were annotated. Results A total of 165,007 high-quality SLAF tags, with an average depth of 47.90× in the parents and 50.78× in F2 individuals, were sequenced. In addition, a total of 137,741 SNPs were detected: 113,311 and 98,861 SNPs in the male and female parent, respectively. A correlation analysis by SNP-index and ED initially located the candidate gene on 1.35 Mb of chrD05, and 20 candidate genes were identified. These genes were involved in genetic variations, single base mutations, insertions, and deletions. Moreover, 42 InDel markers of the whole genome resequencing were also detected. Conclusions In this study, associated markers identified by super-BSA could accelerate the study of CMS in cotton, and as well as in other crops. Some of the 20 genes’ preliminary characteristics provided useful information for further studies on CMS crops. Electronic supplementary material The online version of this article (10.1186/s12864-017-4406-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Cunpeng Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Guiyuan Zhao
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Zhao Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Zhaoxiao Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Kaihui Wang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Suen Liu
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Hanshuang Zhang
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China
| | - Baosheng Guo
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China.
| | - Junyi Geng
- Institute of Cotton, Hebei Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Cotton in Huanghuaihai Semiarid Area, The Ministry of Agriculture, No.598 Heping west, Shijiazhuang, Hebei, 050051, China.
| |
Collapse
|
8
|
Guo X, Guo Y, Ma J, Wang F, Sun M, Gui L, Zhou J, Song X, Sun X, Zhang T. Mapping heterotic loci for yield and agronomic traits using chromosome segment introgression lines in cotton. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:759-74. [PMID: 23570369 DOI: 10.1111/jipb.12054] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 03/14/2013] [Indexed: 05/12/2023]
Abstract
In the present study, a set of chromosome segment introgression lines (CSILs) using Gossypium hirsutum L. TM-1 as the recipient parent and G. barbadense Hai7124 as the donor parent were used to explore the genetic basis of heterosis for interspecific hybrids. Two sets of F₁ populations individually derived from CSILs crossing with both parents were configured to investigate heterotic loci (HL) and substitution effect loci (SL). A total of 58 HL and 39 SL were identified in 3 years. One stable HL, hLP-A4-3, could be detected in all 3 years. Three HLs, hBS-A8-1, hLP-D6-1, and hSI-D7-11, could be detected in 2 years. Four SLs, sBS-D7-1, sLP-A8-1, sLP-D7-1, and sLP-D12-1, could be detected in 2 years. HL and SL tended to be distributed in some HL-rich chromosome segments with close positions. Compared with QTL detected in a former study, HL showed little overlap with QTL, indicating that trait phenotype and heterosis might be controlled by different sets of loci. All three forms of genetic effects (partial-, full-, over-dominant) were identified, while the over-dominant effect made the main contribution to heterosis. These results may help lay the foundation for clarifying the heredity mechanism of heterosis in cotton.
Collapse
Affiliation(s)
- Xian Guo
- College of Agronomy/National Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an 271018, China
| | | | | | | | | | | | | | | | | | | |
Collapse
|