1
|
Shahwar D, Khan Z, Park Y. Molecular Marker-Assisted Mapping, Candidate Gene Identification, and Breeding in Melon ( Cucumis melo L.): A Review. Int J Mol Sci 2023; 24:15490. [PMID: 37895169 PMCID: PMC10607903 DOI: 10.3390/ijms242015490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Melon (Cucumis melo L.) is an important crop that is cultivated worldwide for its fleshy fruit. Understanding the genetic basis of a plant's qualitative and quantitative traits is essential for developing consumer-favored varieties. This review presents genetic and molecular advances related to qualitative and quantitative phenotypic traits and biochemical compounds in melons. This information guides trait incorporation and the production of novel varieties with desirable horticultural and economic characteristics and yield performance. This review summarizes the quantitative trait loci, candidate genes, and development of molecular markers related to plant architecture, branching patterns, floral attributes (sex expression and male sterility), fruit attributes (shape, rind and flesh color, yield, biochemical compounds, sugar content, and netting), and seed attributes (seed coat color and size). The findings discussed in this review will enhance demand-driven breeding to produce cultivars that benefit consumers and melon breeders.
Collapse
Affiliation(s)
- Durre Shahwar
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
| | - Zeba Khan
- Center for Agricultural Education, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh 202002, India;
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, Republic of Korea;
- Life and Industry Convergence Research Institute, Pusan National University, Miryang 50463, Republic of Korea
| |
Collapse
|
2
|
Hong JE, Hossain MR, Jung HJ, Nou IS. QTL associated with Gummy Stem Blight (GSB) resistance in watermelon. BMC Genomics 2022; 23:632. [PMID: 36057546 PMCID: PMC9441027 DOI: 10.1186/s12864-022-08849-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/16/2022] [Indexed: 12/03/2022] Open
Abstract
Background Gummy stem blight (GSB), caused by Didymella bryoniae (syn. Stagonosporopsis cucurbitacearum), produces devastating symptoms on whole plants of watermelon (Citrullus lanatus) and other cucurbits, significantly reducing yield and quality. Identification of genetic determinants and sources of resistance to this devastating GSB disease in watermelon is essential for developing resistant varieties. Results In this study, we aimed at identifying quantitative trait loci (QTLs) linked to GSB resistance in melon. We identified the genome-wide single nucleotide polymorphisms (SNPs) by genotyping by sequencing (GBS) of an F2 population developed from C. lanatus lines, ‘PI 279461’ (resistant) ✕ ‘PI 223764’ (susceptible). Inheritance analysis indicated that resistance to GSB is a multi-genic trait in this population. Three QTLs namely, ClGSB1.1, ClGSB10.1, and ClGSB11.1 associated with GSB resistance, explaining approximately 10% of the phenotypic variation, were identified. Among these, the QTL ClGSB1.1 on chromosome 1 is identified as a major QTL harboring five candidate genes associated with GSB resistance including two RLKs (ClC01G014900 and ClC01G015010), two WRKY transcription factors (ClC01G014910 and ClC01G014990), and one AvrRpt-cleavage domain protein (ClC01G015130). Conclusion Two high resolution melting (HRM) markers, WmGSB1.1–2 and WmGSB1.1–7 having a high positive correlation with the phenotypic variations, were developed. Five potential candidate genes were predicted to be associated with GSB resistance. These findings will help breeders to develop watermelon cultivars resistant to GSB. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08849-2.
Collapse
Affiliation(s)
- Jeong-Eui Hong
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Korea
| | - Mohammad Rashed Hossain
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Hee-Jeong Jung
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Korea
| | - Ill-Sup Nou
- Department of Horticulture, Sunchon National University, 255 Jungang-ro, Suncheon, Jeonnam, 57922, Korea.
| |
Collapse
|
3
|
Zhao Y, Sun Y, Cao K, Zhang X, Bian J, Han C, Jiang Y, Xu L, Wang X. Combined use of specific length amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) for rapid identification of genes influencing fiber content of hemp (Cannabis sativa L.). BMC PLANT BIOLOGY 2022; 22:250. [PMID: 35596150 PMCID: PMC9123736 DOI: 10.1186/s12870-022-03594-w] [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: 08/17/2021] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Hemp (Cannabis sativa L.), an ancient crop, is a significant source of high-quality fiber that primarily caters to the textile industry worldwide. Fiber content is a crucial quantitative trait for evaluating fiber yield in hemp. Understanding the genetic mechanisms involved in hemp breeding is essential for improving yield. In this study, we developed 660 F1 plants from a cross between Jindao-15 (high fiber content fiber-use variety) and Fire No.1 (low fiber content fiber-use variety), and thirty plants each with high and low fiber content were selected from 305 monoecious plants of this population according to 5%-10% of population size for quantitative traits. The DNA from these plants was extracted to establish two bulk DNA pools and then subjected to the restriction digestion by the enzymes RsaI and HaeIII to obtain 314-364 bp digestion fragments and subjected to sequencing using specific length amplified fragment sequencing (SLAF-seq). Finally, we successfully developed 368,404 SLAF tags, which led to the detection of 25,133 high-quality SNPs. Combing with the resequencing results of parents, the SNPs of mixed pools were then subjected to the SNP-Index correlation algorithm, which revealed four candidate regions related to fiber content traits on Chromosome 1, with a length of 8.68 Mb and containing 389 annotated genes. The annotation information and the comparison results identified 15 genes that were highly likely to modulate the fiber content of hemp. Further, qPCR validation identified six genes (LOC115705530, LOC115705875, LOC115704794, LOC115705371, LOC115705688 and LOC115707511) that were highly positively correlated with influencing the hemp fiber content. These genes were involved in the transcription regulation, auxin and water transportion, one carbon and sugar metabolism. And non-synnoumous mutation SNPs which may play vital role in influencing the fiber content were detected in LOC115705875, LOC115704794, LOC115705688 and LOC115707511. Thus, our study highlights the importance of the combined use of SLAF-Seq and Bulked Segregant analysis (BSA) to locate genes related to hemp fiber content rapidly. Hence, our study provides novel mechanistic inputs for the fast identification of genes related to important agronomic traits of hemp and other crops catering to the textile industry.
Collapse
Affiliation(s)
- Yue Zhao
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China
| | - Yufeng Sun
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China
| | - Kun Cao
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China
| | - Xiaoyan Zhang
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China
| | - Jing Bian
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China
| | - Chengwei Han
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China
| | - Ying Jiang
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China
| | - Lei Xu
- Daqing Branch of Heilongjiang Academy of Agricultural Sciences, Heilongjiang, China
| | - Xiaonan Wang
- Daqing Branch of Heilongjiang Academy of Sciences, Heilongjiang, China.
| |
Collapse
|
4
|
Hu Z, Shi X, Chen X, Zheng J, Zhang A, Wang H, Fu Q. Fine-mapping and identification of a candidate gene controlling seed coat color in melon (Cucumis melo L. var. chinensis Pangalo). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:803-815. [PMID: 34825925 DOI: 10.1007/s00122-021-03999-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
MELO3C019554 encoding a homeobox protein (PHD transcription factor) is a candidate gene that involved in the formation of seed coat color in melon. Seed coat color is related to flavonoid content which is closely related to seed dormancy. According to the genetic analysis of a six-generation population derived from two parents (IC2508 with a yellow seed coat and IC2518 with a brown seed coat), we discovered that the yellow seed coat trait in melon is controlled by a single dominant gene, named CmBS-1. Bulked segregant analysis sequencing (BSA-Seq) revealed that the gene is located at 11,860,000-15,890,000 bp (4.03 Mb) on Chr 6. The F2 population was genotyped using insertion-deletions (InDels), from which cleaved amplified polymorphic sequence (dCAPS) markers were derived to construct a genetic map. The gene was then fine-mapped to a 233.98 kb region containing 12 genes. Based on gene sequence analysis with two parents, we found that the MELO3C019554 gene encoding a homeobox protein (PHD transcription factor) had a nonsynonymous single nucleotide polymorphism (SNP) mutation in the coding sequence (CDS), and the SNP mutation resulted in the conversion of an amino acid (A → T) at residue 534. In addition, MELO3C019554 exhibited lower relative expression levels in the yellow seed coat than in the brown seed coat. Furthermore, we found that MELO3C019554 is related to 12 flavonoid metabolites. Thus, we predicted that MELO3C019554 is a candidate gene controlling seed coat color in melon. The study lays a foundation for further cloning projects and functional analysis of this gene, as well as marker-assisted selection breeding.
Collapse
Affiliation(s)
- 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, Beijing, 100081, China
| | - Xueyin Shi
- 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, Beijing, 100081, China
| | - Xuemiao Chen
- 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, Beijing, 100081, 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, Beijing, 100081, 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, Beijing, 100081, 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, Beijing, 100081, 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, Beijing, 100081, China.
| |
Collapse
|
5
|
Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
Collapse
Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| |
Collapse
|
6
|
Li J, Yu X, Zhang S, Yu Z, Li J, Jin X, Zhang X, Yang D. Identification of starch candidate genes using SLAF-seq and BSA strategies and development of related SNP-CAPS markers in tetraploid potato. PLoS One 2021; 16:e0261403. [PMID: 34932571 PMCID: PMC8691606 DOI: 10.1371/journal.pone.0261403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/01/2021] [Indexed: 11/25/2022] Open
Abstract
Potato starch is an essential nutrient for humans and is widely used worldwide. Locating relevant genomic regions, mining stable genes and developing candidate gene markers can promote the breeding of new high-starch potato varieties. A total of 106 F1 individuals and their parents (YSP-4 × MIN-021) were used as test materials, from which 20 plants with high starch content and 20 with low starch content were selected to construct DNA pools for site-specific amplified fragment sequencing (SLAF-seq) and bulked segregation analysis (BSA). A genomic region related to the starch traits was first identified in the 0–5.62 Mb of chromosome 2 in tetraploid potato. In this section, a total of 41 non-synonymous genes, which were considered as candidate genes related to the starch trait, were annotated through a basic local alignment search tool (BLAST) search of multiple databases. Six candidate genes for starch (PGSC0003DMG400017793, PGSC0003DMG400035245, PGSC0003DMG400036713, PGSC0003DMG400040452, PGSC0003DMG400006636 and PGSC0003DMG400044547) were further explored. In addition, cleaved amplified polymorphic sequence (CAPS) markers were developed based on single nucleotide polymorphism (SNP) sites associated with the starch candidate genes. SNP-CAPS markers chr2-CAPS6 and chr2-CAPS21 were successfully developed and validated with the F2 population and 24 tetraploid potato varieties (lines). Functional analysis and cloning of the candidate genes associated with potato starch will be performed in further research, and the SNP-CAPS markers chr2-CAPS6 and chr2-CAPS21 can be further used in marker-assisted selection breeding of tetraploid potato varieties with high starch content.
Collapse
Affiliation(s)
- Jiaqi Li
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xiaoxia Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Sheng Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- * E-mail: (SZ); (ZY)
| | - Zhuo Yu
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
- * E-mail: (SZ); (ZY)
| | - Jingwei Li
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xinghong Jin
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Xia Zhang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| | - Dongsheng Yang
- Agricultural College, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China
| |
Collapse
|
7
|
Kaur G, Pathak M, Singla D, Chhabra G, Chhuneja P, Kaur Sarao N. Quantitative Trait Loci Mapping for Earliness, Fruit, and Seed Related Traits Using High Density Genotyping-by-Sequencing-Based Genetic Map in Bitter Gourd ( Momordica charantia L.). FRONTIERS IN PLANT SCIENCE 2021; 12:799932. [PMID: 35211132 PMCID: PMC8863046 DOI: 10.3389/fpls.2021.799932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/28/2021] [Indexed: 05/17/2023]
Abstract
Bitter gourd (Momordica charantia L.) is an important vegetable crop having numerous medicinal properties. Earliness and yield related traits are main aims of bitter gourd breeding program. High resolution quantitative trait loci (QTLs) mapping can help in understanding the molecular basis of phenotypic variation of these traits and thus facilitate marker-assisted breeding. The aim of present study was to identify genetic loci controlling earliness, fruit, and seed related traits. To achieve this, genotyping-by-sequencing (GBS) approach was used to genotype 101 individuals of F4 population derived from a cross between an elite cultivar Punjab-14 and PAUBG-6. This population was phenotyped under net-house conditions for three years 2018, 2019, and 2021. The linkage map consisting of 15 linkage groups comprising 3,144 single nucleotide polymorphism (SNP) markers was used to detect the QTLs for nine traits. A total of 50 QTLs for these traits were detected which were distributed on 11 chromosomes. The QTLs explained 5.09-29.82% of the phenotypic variance. The highest logarithm of the odds (LOD) score for a single QTL was 8.68 and the lowest was 2.50. For the earliness related traits, a total of 22 QTLs were detected. For the fruit related traits, a total of 16 QTLs and for seed related traits, a total of 12 QTLs were detected. Out of 50 QTLs, 20 QTLs were considered as frequent QTLs (FQ-QTLs). The information generated in this study is very useful in the future for fine-mapping and marker-assisted selection for these traits in bitter gourd improvement program.
Collapse
Affiliation(s)
- Gurpreet Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Mamta Pathak
- Department of Vegetable Science, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Gautam Chhabra
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Navraj Kaur Sarao
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
- *Correspondence: Navraj Kaur Sarao,
| |
Collapse
|
8
|
Hao N, Han D, Huang K, Du Y, Yang J, Zhang J, Wen C, Wu T. Genome-based breeding approaches in major vegetable crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1739-1752. [PMID: 31728564 DOI: 10.1007/s00122-019-03477-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 11/09/2019] [Indexed: 05/09/2023]
Abstract
Vegetable crops are major nutrient sources for humanity and have been well-cultivated since thousands of years of domestication. With the rapid development of next-generation sequencing and high-throughput genotyping technologies, the reference genome of more than 20 vegetables have been well-assembled and published. Resequencing approaches on large-scale germplasm resources have clarified the domestication and improvement of vegetable crops by human selection; its application on genetic mapping and quantitative trait locus analysis has led to the discovery of key genes and molecular markers linked to important traits in vegetables. Moreover, genome-based breeding has been utilized in many vegetable crops, including Solanaceae, Cucurbitaceae, Cruciferae, and other families, thereby promoting molecular breeding at a single-nucleotide level. Thus, genome-wide SNP markers have been widely used, and high-throughput genotyping techniques have become one of the most essential methods in vegetable breeding. With the popularization of gene editing technology research on vegetable crops, breeding efficiency can be rapidly increased, especially by combining the genomic and variomic information of vegetable crops. This review outlines the present genome-based breeding approaches used for major vegetable crops to provide insights into next-generation molecular breeding for the increasing global population.
Collapse
Affiliation(s)
- Ning Hao
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Deguo Han
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China
| | - Ke Huang
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Yalin Du
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| | - Tao Wu
- College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, China.
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, 150030, China.
| |
Collapse
|
9
|
Ren R, Xu J, Zhang M, Liu G, Yao X, Zhu L, Hou Q. Identification and Molecular Mapping of a Gummy Stem Blight Resistance Gene in Wild Watermelon ( Citrullus amarus) Germplasm PI 189225. PLANT DISEASE 2020; 104:16-24. [PMID: 31730411 DOI: 10.1094/pdis-04-19-0753-re] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Gummy stem blight (GSB), caused by Stagonosporopsis cucurbitacearum (syn. Didymella bryoniae), is a destructive foliar disease of watermelon in areas with hot and humid climates. The wild watermelon germplasm PI 189225 is a known source of resistance to GSB. The identification and use of molecular markers linked to resistance genes in the wild-type germplasm will speed up the introgression of GSB resistance into new watermelon varieties. An F2 segregating population was obtained from a cross between the resistant wild watermelon genotype PI 189225 and the susceptible genotype K3. The F2-derived F3 families were inoculated with a single isolate of S. cucurbitacearum (JS002) from Jiangsu Academy of Agricultural Sciences. The results of the genetic analysis demonstrated that GSB resistance in PI 189225 was controlled by a major quantitative trait locus (QTL), temporarily designated Qgsb8.1. Based on the results of bulk sergeant analysis and sequencing, one associated region spanning 5.7 Mb (10,358,659 to 16,101,517) on chromosome 8 was identified as responsible for the resistance to GSB using the Δ(single-nucleotide polymorphism [SNP]-index) method. The result of a QTL linkage analysis with Kompetitive allele-specific PCR (KASP) SNP markers further mapped the GSB resistance locus between the SNP markers KASP_JS9383 and KASP_JS9168 in a region of 571.27 kb on chromosome 8. According to the watermelon gene annotation database, the region contains approximately 19 annotated genes and, of these 19 genes, 2 are disease resistance gene analogs: Cla001017 (coiled-coil nucleotide-binding site leucine-rich repeat resistance protein) and Cla001019 (pathogenesis related). Reverse-transcription quantitative PCR demonstrated that the expression of the two genes changed following S. cucurbitacearum infection, suggesting that they play important roles in GSB resistance in watermelon. This result will facilitate fine mapping and cloning of the Qgsb8.1 locus, and the linked markers will further provide a useful tool for marker-assisted selection of this locus in watermelon breeding programs.
Collapse
Affiliation(s)
- Runsheng Ren
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Jinhua Xu
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Man Zhang
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Guang Liu
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Xiefeng Yao
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Lingli Zhu
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| | - Qian Hou
- Jiangsu Key Laboratory for Horticultural Crop Genetic, Improvement/Institute of Vegetable, Jiangsu, Academy of Agricultural Sciences, Nanjing, Jiangsu, China
| |
Collapse
|
10
|
McCallum J, Laing W, Bulley S, Thomson S, Catanach A, Shaw M, Knaebel M, Tahir J, Deroles S, Timmerman-Vaughan G, Crowhurst R, Hilario E, Chisnall M, Lee R, Macknight R, Seal A. Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids. PLANTS (BASEL, SWITZERLAND) 2019; 8:E237. [PMID: 31336644 PMCID: PMC6681377 DOI: 10.3390/plants8070237] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/15/2019] [Accepted: 07/16/2019] [Indexed: 12/20/2022]
Abstract
During analysis of kiwifruit derived from hybrids between the high vitamin C (ascorbic acid; AsA) species Actinidia eriantha and A. chinensis, we observed bimodal segregation of fruit AsA concentration suggesting major gene segregation. To test this hypothesis, we performed whole-genome sequencing on pools of hybrid genotypes with either high or low AsA fruit. Pool-GWAS (genome-wide association study) revealed a single Quantitative Trait Locus (QTL) spanning more than 5 Mbp on chromosome 26, which we denote as qAsA26.1. A co-dominant PCR marker was used to validate this association in four diploid (A. chinensis × A. eriantha) × A. chinensis backcross families, showing that the A. eriantha allele at this locus increases fruit AsA levels by 250 mg/100 g fresh weight. Inspection of genome composition and recombination in other A. chinensis genetic maps confirmed that the qAsA26.1 region bears hallmarks of suppressed recombination. The molecular fingerprint of this locus was examined in leaves of backcross validation families by RNA sequencing (RNASEQ). This confirmed strong allelic expression bias across this region as well as differential expression of transcripts on other chromosomes. This evidence suggests that the region harbouring qAsA26.1 constitutes a supergene, which may condition multiple pleiotropic effects on metabolism.
Collapse
Affiliation(s)
- John McCallum
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand.
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand.
| | - William Laing
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Sean Bulley
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Susan Thomson
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Andrew Catanach
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Martin Shaw
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Mareike Knaebel
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Jibran Tahir
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Simon Deroles
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 11600, Palmerston North 4442, New Zealand
| | - Gail Timmerman-Vaughan
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 4704, Christchurch 8140, New Zealand
| | - Ross Crowhurst
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Elena Hilario
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand
| | - Matthew Chisnall
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Robyn Lee
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Richard Macknight
- Biochemistry Department, University of Otago, Dunedin 9054, New Zealand
| | - Alan Seal
- New Cultivar Innovation, The New Zealand Institute for Plant & Food Research Limited, 412 No 1 Road, RD 2 Te Puke 3182, New Zealand
| |
Collapse
|
11
|
Pujol M, Alexiou KG, Fontaine AS, Mayor P, Miras M, Jahrmann T, Garcia-Mas J, Aranda MA. Mapping Cucumber Vein Yellowing Virus Resistance in Cucumber ( Cucumis sativus L.) by Using BSA-seq Analysis. FRONTIERS IN PLANT SCIENCE 2019; 10:1583. [PMID: 31850047 PMCID: PMC6901629 DOI: 10.3389/fpls.2019.01583] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/12/2019] [Indexed: 05/14/2023]
Abstract
Cucumber vein yellowing virus (CVYV) causes severe yield losses in cucurbit crops across Mediterranean countries. The control of this virus is based on cultural practices to prevent the presence of its vector (Bemisia tabaci) and breeding for natural resistance, which requires the identification of the loci involved and the development of molecular markers for linkage analysis. In this work, we mapped a monogenic locus for resistance to CVYV in cucumber by using a Bulked Segregant Analysis (BSA) strategy coupled with whole-genome resequencing. We phenotyped 135 F3 families from a segregating population between a susceptible pickling cucumber and a resistant Long Dutch type cucumber for CVYV resistance. Phenotypic analysis determined the monogenic and incomplete dominance inheritance of the resistance. We named the locus CsCvy-1. For mapping this locus, 15 resistant and 15 susceptible homozygous F2 individuals were selected for whole genome resequencing. By using a customized bioinformatics pipeline, we identified a unique region in chromosome 5 associated to resistance to CVYV, explaining more than 80% of the variability. The resequencing data provided us with additional SNP markers to decrease the interval of CsCvy-1 to 625 kb, containing 24 annotated genes. Markers flanking CsCvy-1 in a 5.3 cM interval were developed for marker-assisted selection (MAS) in breeding programs and will be useful for the identification of the target gene in future studies.
Collapse
Affiliation(s)
- Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Plant and Animal Genomics Program, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Genomics and Biotecnology Program, Barcelona, Spain
| | - Konstantinos G. Alexiou
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Plant and Animal Genomics Program, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Genomics and Biotecnology Program, Barcelona, Spain
| | | | - Patricia Mayor
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, Murcia, Spain
| | - Manuel Miras
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, Murcia, Spain
| | - Torben Jahrmann
- Semillas Fitó S.A., Biotechnology Department, Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Plant and Animal Genomics Program, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Genomics and Biotecnology Program, Barcelona, Spain
| | - Miguel A. Aranda
- Centro de Edafología y Biología Aplicada del Segura (CEBAS)-CSIC, Departamento de Biología del Estrés y Patología Vegetal, Murcia, Spain
- *Correspondence: Miguel A. Aranda,
| |
Collapse
|
12
|
Wang G, Chen B, Du H, Zhang F, Zhang H, Wang Y, He H, Geng S, Zhang X. Genetic mapping of anthocyanin accumulation-related genes in pepper fruits using a combination of SLAF-seq and BSA. PLoS One 2018; 13:e0204690. [PMID: 30261055 PMCID: PMC6160195 DOI: 10.1371/journal.pone.0204690] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/11/2018] [Indexed: 12/22/2022] Open
Abstract
Anthocyanins have significant functions in stress tolerance in pepper (Capsicum annuum L.) and also benefit human health. Nevertheless, the key structural genes and regulatory genes involved in anthocyanin accumulation in pepper fruits are still not well understood and fine mapped. For the present study, 383 F2 plants from a cross between the green-fruited C. annuum line Z5 and the purple-fruited line Z6 was developed. Two separate bulked DNA pools were constructed with DNAs extracted from either 37 plants with high anthocyanin content or from 18 plants with no anthocyanin. A combination of specific-locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was used to identify candidates for regions associated with anthocyanin accumulation. We identified a total of 127,004 high-quality single nucleotide polymorphism (SNP) markers, and detected 1674 high-quality SNP markers associated with anthocyanin accumulation. Three candidate anthocyanin-associated regions including the intervals from 12.48 to 20.00 Mb, from 54.67 to 56.59 Mb, and from 192.17 to 196.82 Mb were identified within a 14.10-Mb interval on chromosome 10 containing 126 candidate genes. Based on their annotations, we identified 12 candidate genes that are predicted to be associated with anthocyanin expression. The present results provide an efficient strategy for genetic mapping of and valuable insights into the genetic mechanisms of anthocyanin accumulation in pepper fruit, and allow us to clone and functionally analyze the genes that influence anthocyanin accumulation in this species.
Collapse
Affiliation(s)
- Guoyun Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Haiying Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Yaqin Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Hongju He
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
| | - Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (XZ)
| |
Collapse
|
13
|
Zhang X, Wang G, Chen B, Du H, Zhang F, Zhang H, Wang Q, Geng S. Candidate genes for first flower node identified in pepper using combined SLAF-seq and BSA. PLoS One 2018; 13:e0194071. [PMID: 29558466 PMCID: PMC5860747 DOI: 10.1371/journal.pone.0194071] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 02/23/2018] [Indexed: 02/05/2023] Open
Abstract
First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.), but the genetic mechanisms that control FFN are still poorly understood. In the present study, we developed 249 F2 plants derived from an intraspecific cross between the inbred pepper lines Z4 and Z5. Thirty plants with the highest FFN and 30 plants with the lowest FFN were chosen and their DNAs were pooled according to phenotype to construct two bulked DNA pools. Specific-locus amplified fragment sequencing (SLAF-seq) was combined with bulked segregant analysis (BSA) to identify candidate regions related to FFN. According to our genetic analysis, the FFN trait is quantitatively inherited. A total of 106,848 high-quality single nucleotide polymorphism (SNP) markers were obtained, and 393 high-quality SNP markers associated with FFN were detected. Ten candidate regions within an interval of 3.98 Mb on chromosome 12 harboring 23 candidate genes were identified as closely correlated with FFN. Five genes (CA12g15130, CA12g15160, CA12g15370, CA12g15360, and CA12g15390) are predicted based on their annotations to be associated with expression of the FFN trait. The present study demonstrates an efficient genetic mapping strategy and lays a good foundation for molecular marker-assisted breeding using SNP markers linked to FFN and for cloning and functional analysis of the key genes controlling FFN.
Collapse
Affiliation(s)
- Xiaofen Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- College of Horticulture, China Agricultural University, Beijing, P.R. China
| | - Guoyun Wang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Bin Chen
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Heshan Du
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Fenglan Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Haiying Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
| | - Qian Wang
- College of Horticulture, China Agricultural University, Beijing, P.R. China
- * E-mail: (SG); (QW)
| | - Sansheng Geng
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing, P.R. China
- * E-mail: (SG); (QW)
| |
Collapse
|
14
|
Yang H, Zhao T, Jiang J, Wang S, Wang A, Li J, Xu X. Mapping and screening of the tomato Stemphylium lycopersici resistance gene, Sm, based on bulked segregant analysis in combination with genome resequencing. BMC PLANT BIOLOGY 2017; 17:266. [PMID: 29284401 PMCID: PMC5747103 DOI: 10.1186/s12870-017-1215-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 12/18/2017] [Indexed: 05/26/2023]
Abstract
BACKGROUND Tomato gray leaf spot disease caused by Stemphylium lycopersici (S. lycopersici) is considered one of the major diseases of cultivated tomatoes. The only S. lycopersici resistance gene, Sm, was derived from the wild tomato species S. pimpinellifolium. Sm has been identified as an effective source of gray leaf spot resistance in tomatoes and has been mapped to tomato chromosome 11. In this study, the first bulked segregant analysis (BSA) combined with genome resequencing for the mapping and screening of the Sm candidate gene was performed. RESULTS Based on the resequencing results, we identified 50,968 Diff-markers, most of which were distributed on chromosome 11. A total of 37 genes were located in the interval of 0.26-Mb. The gene loci of resistant and susceptible lines were sequenced successfully using PCR products. The relative expression levels of candidate genes in resistant and susceptible lines were confirmed via qRT-PCR, Solyc11g011870.1.1 and Solyc11g011880.1.1 were identified through qRT-PCR. A marker, D5, which was cosegregated with the resistant locus, was identified according to the mutation of the Solyc11g011880.1.1 trait in the resistant line. CONCLUSIONS The Sm gene was mapped to the short arm of chromosome 11. The candidate genes Solyc11g011870.1.1 and Solyc11g011880.1.1 displayed expression patterns related to the resistance response. This study will be valuable for Sm cloning and Sm gene breeding in tomato.
Collapse
Affiliation(s)
- Huanhuan Yang
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | - Tingting Zhao
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | - Jingbin Jiang
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | | | - Aoxue Wang
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China
| | - Jingfu Li
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China.
| | - Xiangyang Xu
- College of Horticulture, Northeast Agricultural University, Mucai Street 59, Xiangfang District Harbin, 150030, China.
| |
Collapse
|
15
|
Genome-Wide Linkage-Disequilibrium Mapping to the Candidate Gene Level in Melon (Cucumis melo). Sci Rep 2017; 7:9770. [PMID: 28852011 PMCID: PMC5575340 DOI: 10.1038/s41598-017-09987-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 08/01/2017] [Indexed: 12/22/2022] Open
Abstract
Cucumis melo is highly diverse for fruit traits providing wide breeding and genetic research opportunities, including genome-wide association (GWA) analysis. We used a collection of 177 accessions representing the two C. melo subspecies and 11 horticultural groups for detailed characterization of fruit traits variation and evaluation of the potential of GWA for trait mapping in melon. Through genotyping-by-sequencing, 23,931 informative SNPs were selected for genome-wide analyses. We found that linkage-disequilibrium decays at ~100 Kb in this collection and that population structure effect on association results varies between traits. We mapped several monogenic traits to narrow intervals overlapping with known causative genes, demonstrating the potential of diverse collections and GWA for mapping Mendelian traits to a candidate-gene level in melon. We further report on mapping of fruit shape quantitative trait loci (QTLs) and comparison with multiple previous QTL studies. Expansion of sample size and a more balanced representation of taxonomic groups might improve efficiency for simple traits dissection. But, as in other plant species, integrated linkage-association multi-allelic approaches are likely to produce better combination of statistical power, diversity capture and mapping resolution in melon. Our data can be utilized for selection of the most appropriate accessions for such approaches.
Collapse
|
16
|
Sheng Y, Wang Y, Jiao S, Jin Y, Ji P, Luan F. Mapping and Preliminary Analysis of ABORTED MICROSPORES ( AMS) as the Candidate Gene Underlying the Male Sterility ( MS-5) Mutant in Melon ( Cucumis melo L.). FRONTIERS IN PLANT SCIENCE 2017; 8:902. [PMID: 28611814 PMCID: PMC5447745 DOI: 10.3389/fpls.2017.00902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 05/15/2017] [Indexed: 05/06/2023]
Abstract
Melon is an important agricultural and economic vegetable crop worldwide. The genetic male sterility mutant (ms-5) has a recessive nuclear gene that controls the male sterility germplasm. Male sterility could reduce the cost of F1 seed production in melon, but heterozygous fertile plants should be removed before pollination. In this study, bulked segregant analysis combined with specific length amplified fragment sequencing was applied to map the single nuclear male sterility recessive gene. A 30-kb candidate region on chromosome 9 located on scaffold 000048 and spanning 2,522,791 to 2,555,104 bp was identified and further confirmed by cleavage amplified polymorphic sequence markers based on parental line resequencing data and classical mapping of 252 F2 individuals. Gene prediction indicated that six annotated genes are present in the 30-kb candidate region. Quantitative RT-PCR revealed significant differences in the expression level of the LOC103498166 ABORTED MICROSPORES (AMS) gene in male-sterile lines (ms-5) and male-fertile (HM1-1) lines during the 2-mm (tetrad) and 5-mm (the first pollen mitosis) periods, and negative regulation of the AMS candidate gene transcription factor was also detected. Sequencing and cluster analysis of the AMS transcription factor revealed five single-nucleotide polymorphisms between the parental lines. The data presented herein suggest that the AMS transcription factor is a possible candidate gene for single nuclear male sterility in melon. The results of this study will help breeders to identify male-sterile and -fertile plants at seeding as marker-assisted selection methods, which would reduce the cost of seed production and improve the use of male-sterile lines in melon.
Collapse
Affiliation(s)
- Yunyan Sheng
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture/Northeast Agricultural UniversityHarbin, China
- *Correspondence: Yunyan Sheng,
| | - Yudan Wang
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Shiqi Jiao
- Department of Horticulture, Northeast Agricultural UniversityHarbin, China
| | - Yazhong Jin
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Peng Ji
- Department of Agriculture, Heilongjiang Bayi Agricultural UniversityDaqing, China
| | - Feishi Luan
- Department of Horticulture, Northeast Agricultural UniversityHarbin, China
| |
Collapse
|