1
|
Yu D, Huang R, Yu S, Liang Q, Wang Y, Dang H, Zhang Y. Construction of the first high-density genetic linkage map and QTL mapping of flavonoid and leaf-size related traits in Epimedium. BMC PLANT BIOLOGY 2023; 23:278. [PMID: 37231361 DOI: 10.1186/s12870-023-04257-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 04/28/2023] [Indexed: 05/27/2023]
Abstract
BACKGROUND Leaves are the main medicinal organ in Epimedium herbs, and leaf flavonoid content is an important criterion of Epimedium herbs. However, the underlying genes that regulate leaf size and flavonoid content are unclear, which limits the use of breeding for Epimedium development. This study focuses on QTL mapping of flavonoid and leaf-size related traits in Epimedium. RESULTS We constructed the first high-density genetic map (HDGM) using 109 F1 hybrids of Epimedium leptorrhizum and Epimedium sagittatum over three years (2019-2021). Using 5,271 single nucleotide polymorphism (SNP) markers, an HDGM with an overall distance of 2,366.07 cM and a mean gap of 0.612 cM was generated by utilizing genotyping by sequencing (GBS) technology. Every year for three years, 46 stable quantitative trait loci (QTLs) for leaf size and flavonoid contents were discovered, including 31 stable loci for Epimedin C (EC), one stable locus for total flavone content (TFC), 12 stable loci for leaf length (LL), and two stable loci for leaf area (LA). For flavonoid content and leaf size, the phenotypic variance explained for these loci varied between 4.00 and 16.80% and 14.95 and 17.34%, respectively. CONCLUSIONS Forty-six stable QTLs for leaf size and flavonoid content traits were repeatedly detected over three years. The HDGM and stable QTLs are laying the basis for breeding and gene investigation in Epimedium and will contribute to accelerating the identification of desirable genotypes for Epimedium breeding.
Collapse
Affiliation(s)
- Dongyue Yu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P.R. China
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
| | - Ruoqi Huang
- University of Chinese Academy of Sciences, Beijing, 100049, P.R. China
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Shuxia Yu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Qiong Liang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, P.R. China
| | - Haishan Dang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P.R. China.
| | - Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, P. R. China.
| |
Collapse
|
2
|
Guan W, Ke C, Tang W, Jiang J, Xia J, Xie X, Yang M, Duan C, Wu W, Zheng Y. Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant. Int J Mol Sci 2022; 23:ijms231810258. [PMID: 36142175 PMCID: PMC9499331 DOI: 10.3390/ijms231810258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 02/08/2023] Open
Abstract
High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F2 plants from an interspecific cross (Solanum melongena × S. incanum) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F2:3 lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL.
Collapse
Affiliation(s)
- Wenxiang Guan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changjiao Ke
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiqi Tang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jialong Jiang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Xia
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaofang Xie
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei Yang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chenfeng Duan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
| | - Yan Zheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
| |
Collapse
|
3
|
Chen T, Hu L, Wang S, Wang L, Cheng X, Chen H. Construction of High-Density Genetic Map and Identification of a Bruchid Resistance Locus in Mung Bean (Vigna radiata L.). Front Genet 2022; 13:903267. [PMID: 35873485 PMCID: PMC9305327 DOI: 10.3389/fgene.2022.903267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Mung bean (Vigna radiata L.) is an economically important grain legume cultivated in Asian countries. High-density genetic linkage is a valuable and effective tool for mapping quantitative trait loci (QTL). In the current study, a high-resolution genetic map containing 4,180 single-nucleotide polymorphisms (SNPs) was assigned to 11 linkage groups (LGs) and spanning 1,751.39 cM in length was constructed for mung bean, and the average distance between adjacent markers was 0.42 cM. Bruchids (Callosobruchus spp.) cause significant damage to and loss of legume seeds. A locus for bruchid resistance was detected. The gene Vradi05g03810, encoding a probable resistance-specific protein, was found to be the most likely key candidate gene in mung beans. A 69-bp sequence deletion was identified in the coding region by comparing the cDNA sequences of bruchid-resistant and bruchid-susceptible lines. This SNP-based high-density linkage map is one of the first to be constructed across the mung bean genome. This map will not only facilitate the genetic mapping of genes or complex loci that control important agronomic traits but also offer a tool for promoting future genetics and comparative genomic studies in Vigna.
Collapse
|
4
|
Tao J, Li S, Wang Q, Yuan Y, Ma J, Xu M, Yang Y, Zhang C, Chen L, Sun Y. Construction of a high-density genetic map based on specific-locus amplified fragment sequencing and identification of loci controlling anthocyanin pigmentation in Yunnan red radish. HORTICULTURE RESEARCH 2022; 9:uhab031. [PMID: 35043168 PMCID: PMC8829420 DOI: 10.1093/hr/uhab031] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 01/19/2022] [Accepted: 10/23/2021] [Indexed: 06/14/2023]
Abstract
Radish (Raphanus sativus L.) belongs to the family Brassicaceae. The Yunnan red radish variety contains fairly relatively large amounts of anthocyanins, making them important raw materials for producing edible red pigment. However, the genetic mechanism underlying this pigmentation has not been fully characterized. Herein, the radish inbred line YAAS-WR1 (white root-skin and white root-flesh) was crossed with the inbred line YAAS-RR1 (red root-skin and red root-flesh) to produce F1, F2, BC1P1, and BC1P2 populations. Genetic analyses revealed that the pigmented/non-pigmented (PiN) and purple/red (PR) traits were controlled by two genetic loci. The F2 population and the specific-locus amplified fragment sequencing (SLAF-seq) technique were used to construct a high-density genetic map (1230.16 cM), which contained 4032 markers distributed in nine linkage groups, with a mean distance between markers of 0.31 cM. Additionally, two QTL (QAC1 and QAC2) considerably affecting radish pigmentation were detected. A bioinformatics analysis of the QAC1 region identified 58 predicted protein-coding genes. Of these genes, RsF3'H, which is related to anthocyanin biosynthesis, was revealed as a likely candidate gene responsible for the PR trait. The results were further verified by analyzing gene structure and expression. Regarding QAC2, RsMYB1.3 was determined to be a likely candidate gene important for the PiN trait, with a 4-bp insertion in the first exon that introduced a premature termination codon in the YAAS-WR1 sequence. Assays demonstrated that RsMYB1.3 interacted with RsTT8 and activates RsTT8 and RsUFGT expression. These findings may help clarify the complex regulatory mechanism underlying radish anthocyanin synthesis. Furthermore, this study's results may be relevant for the molecular breeding of radish to improve the anthocyanin content and appearance of the taproots.
Collapse
Affiliation(s)
- Jing Tao
- College of Agronomy and Biotechnology, Yunnan Agriculture University, 452 Fengyuan Road, Kunming, 650201, China
- Engineering Research Center of Vegetable Germplasm Innovation and Support Production Technology, Horticultural Research Institute, Yunnan Academy of Agricultural Sciences; 2238 Beijing Road, Kunming, 650205, China
| | - Shikai Li
- Engineering Research Center of Vegetable Germplasm Innovation and Support Production Technology, Horticultural Research Institute, Yunnan Academy of Agricultural Sciences; 2238 Beijing Road, Kunming, 650205, China
| | - Qian Wang
- Engineering Research Center of Vegetable Germplasm Innovation and Support Production Technology, Horticultural Research Institute, Yunnan Academy of Agricultural Sciences; 2238 Beijing Road, Kunming, 650205, China
| | - Yi Yuan
- Engineering Research Center of Vegetable Germplasm Innovation and Support Production Technology, Horticultural Research Institute, Yunnan Academy of Agricultural Sciences; 2238 Beijing Road, Kunming, 650205, China
| | - Jiqiong Ma
- Key Lab of Agricultural Biotechnology of Yunnan Province, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation of Ministry of Agriculture, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, 2238 Beijing Road, Kunming, 650205, China
| | - Minghui Xu
- Key Lab of Agricultural Biotechnology of Yunnan Province, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation of Ministry of Agriculture, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, 2238 Beijing Road, Kunming, 650205, China
| | - Yi Yang
- Key Lab of Agricultural Biotechnology of Yunnan Province, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation of Ministry of Agriculture, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, 2238 Beijing Road, Kunming, 650205, China
| | - Cui Zhang
- College of Plant Protection, Yunnan Agricultural University, 452 Fengyuan Road, Kunming, 650201, China
| | - Lijuan Chen
- College of Agronomy and Biotechnology, Yunnan Agriculture University, 452 Fengyuan Road, Kunming, 650201, China
| | - Yiding Sun
- Key Lab of Agricultural Biotechnology of Yunnan Province, Key Lab of Southwestern Crop Gene Resources and Germplasm Innovation of Ministry of Agriculture, Biotechnology and Germplasm Resources Research Institute, Yunnan Academy of Agricultural Sciences, 2238 Beijing Road, Kunming, 650205, China
| |
Collapse
|
5
|
Shimomura K, Sugiyama M, Kawazu Y, Yoshioka Y. Identification of quantitative trait loci for powdery mildew resistance in highly resistant cucumber ( Cucumis sativus L.) using ddRAD-seq analysis. BREEDING SCIENCE 2021; 71:326-333. [PMID: 34776739 PMCID: PMC8573554 DOI: 10.1270/jsbbs.20141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 02/08/2021] [Indexed: 06/13/2023]
Abstract
Powdery mildew, caused by Podosphaera xanthii (syn. Sphaerotheca fuliginea ex Fr. Poll.), is one of the most economically important foliar diseases in cucumber (Cucumis sativus L.). Cucumber parental line 'Kyuri Chukanbohon Nou 5 Go', developed from weedy cucumber line CS-PMR1, is highly resistant to powdery mildew and is promising breeding material. We performed quantitative trait locus (QTL) analysis using double-digest restriction-site-associated DNA sequencing (ddRAD-Seq) in a population from a cross between 'Kyuri Chukanbohon Nou 5 Go' and the Japanese native cultivar 'Kaga-aonaga-fushinari', which is susceptible to powdery mildew. The resistance of the population and its parents was evaluated using leaf disc assays and image analysis. We detected one major QTL on Chr. 5 that was effective at both 20°C and 25°C and one minor QTL on Chr. 1 effective at 20°C. We detected two additional QTLs in subpopulation: one on Chr. 3 effective at 20°C and one on Chr. 5 effective at both 20°C and 25°C in a position different from the major QTL. The resistance alleles at all four QTLs were contributed by 'Kyuri Chukanbohon Nou 5 Go'. The results of this study can be used to develop practical DNA markers tightly linked to genes for powdery mildew resistance.
Collapse
Affiliation(s)
- Koichiro Shimomura
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science (NIVFS), National Agriculture and Food Research Organization (NARO), Kusawa 360, Ano, Tsu, Mie 514-2392, Japan
| | - Yosuke Yoshioka
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| |
Collapse
|
6
|
Li F, Liu J, Liu W, Gao J, Lei Q, Han H, Yang J, Li H, Cao D, Zhou Y. Genome-wide association study of body size traits in Wenshang Barred chickens based on the specific-locus amplified fragment sequencing technology. Anim Sci J 2021; 92:e13506. [PMID: 33398896 DOI: 10.1111/asj.13506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
Chicken body size (BS) is an economically important trait, which has been assessed in many studies for genetic selection. However, previous reports detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) of purebred Wenshang Barred chickens. A total of 250 one-day-old male chickens were assessed in this study. Body size in individual birds was measured at 56 days. SLAF-seq was used to genotype and GWAS analysis was carried out using the general linear model (GLM) of the TASSEL program. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, of which 175,211 were tested as candidate SNPs for genome-wide association analysis using the TASSEL general linear model. Three SNPs markers reached genome-wide significance. Of these, chrZ:81729634, chrZ:81841715, and chrZ:81954149 at 81,729,634, 81,841,715, and 81,954,149 bp of GGA Z were significantly associated with body diagonal length at 56 days (BDL56); and tibia length at 56 days (TL56). These SNPs were close to three genes, including ZCCHC7, PAX5, and MELK. These results open new horizons for studies on BS and should promote the use of Chinese chickens, especially Wenshang Barred chickens.
Collapse
Affiliation(s)
- Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jingchao Yang
- Shandong Animal Husbandry General Station, Ji'nan, P. R. China
| | - Huimin Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| |
Collapse
|
7
|
Mandozai A, Moussa AA, Zhang Q, Qu J, Du Y, Anwari G, Al Amin N, Wang P. Genome-Wide Association Study of Root and Shoot Related Traits in Spring Soybean ( Glycine max L.) at Seedling Stages Using SLAF-Seq. FRONTIERS IN PLANT SCIENCE 2021; 12:568995. [PMID: 34394134 PMCID: PMC8355526 DOI: 10.3389/fpls.2021.568995] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/08/2021] [Indexed: 05/19/2023]
Abstract
Root systems can display variable genetic architectures leading to nutrient foraging or improving abiotic stress tolerance. Breeding for new soybean varieties with efficient root systems has tremendous potential in enhancing resource use efficiency and plant adaptation for challenging climates. In this study, root related traits were analyzed in a panel of 260 spring soybean with genome-wide association study (GWAS). Genotyping was done with specific locus amplified fragment sequencing (SLAF-seq), and five GWAS models (GLM, MLM, CMLM, FaST-LMM, and EMMAX) were used for analysis. A total of 179,960 highly consistent SNP markers distributed over the entire genome with an inter-marker distance of 2.36 kb was used for GWAS analysis. Overall, 27 significant SNPs with a phenotypic contribution ranging from 20 to 72% and distributed on chromosomes 2, 6, 8, 9, 13, 16 and 18 were identified and two of them were found to be associated with multiple root-related traits. Based on the linkage disequilibrium (LD) distance of 9.5 kb for the different chromosomes, 11 root and shoot regulating genes were detected based on LD region of a maximum 55-bp and phenotypic contribution greater than 22%. Expression analysis revealed an association between expression levels of those genes and the degree of root branching number. The current study provides new insights into the genetic architecture of soybean roots, and the underlying SNPs/genes could be critical for future breeding of high-efficient root system in soybean.
Collapse
|
8
|
An Y, Chen L, Tao L, Liu S, Wei C. QTL Mapping for Leaf Area of Tea Plants ( Camellia sinensis) Based on a High-Quality Genetic Map Constructed by Whole Genome Resequencing. FRONTIERS IN PLANT SCIENCE 2021; 12:705285. [PMID: 34394160 PMCID: PMC8358608 DOI: 10.3389/fpls.2021.705285] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 07/07/2021] [Indexed: 05/08/2023]
Abstract
High-quality genetic maps play important roles in QTL mapping and molecular marker-assisted breeding. Tea leaves are not only important vegetative organs but are also the organ for harvest with important economic value. However, the key genes and genetic mechanism of regulating leaf area have not been clarified. In this study, we performed whole-genome resequencing on "Jinxuan," "Yuncha 1" and their 96 F1 hybrid offspring. From the 1.84 Tb of original sequencing data, abundant genetic variation loci were identified, including 28,144,625 SNPs and 2,780,380 indels. By integrating the markers of a previously reported genetic map, a high-density genetic map consisting of 15 linkage groups including 8,956 high-quality SNPs was constructed. The total length of the genetic map is 1,490.81 cM, which shows good collinearity with the genome. A total of 25 representative markers (potential QTLs) related to leaf area were identified, and there were genes differentially expressed in large and small leaf samples near these markers. GWAS analysis further verified the reliability of QTL mapping. Thirty-one pairs of newly developed indel markers located near these potential QTLs showed high polymorphism and had good discrimination between large and small leaf tea plant samples. Our research will provide necessary support and new insights for tea plant genetic breeding, quantitative trait mapping and yield improvement.
Collapse
Affiliation(s)
- Yanlin An
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Linbo Chen
- Yunnan Provincial Key Laboratory of Tea Science, Tea Research Institute, Yunnan Academy of Agricultural Sciences, Menghai, China
| | - Lingling Tao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Shengrui Liu
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
| | - Chaoling Wei
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, China
- *Correspondence: Chaoling Wei,
| |
Collapse
|
9
|
Wang Z, Sun Y, Huang X, Li F, Liu Y, Zhu H, Liu Z, Ke W. Genetic diversity and population structure of eddoe taro in China using genome-wide SNP markers. PeerJ 2020; 8:e10485. [PMID: 33354429 PMCID: PMC7731653 DOI: 10.7717/peerj.10485] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/12/2020] [Indexed: 01/20/2023] Open
Abstract
Taro (Colocasia esculenta) is an important root and tuber crop cultivated worldwide. There are two main types of taro that vary in morphology of corm and cormel, ‘dasheen’ and ‘eddoe’. The eddoe type (Colocasia esculenta var. antiquorium) is predominantly distributed throughout China. Characterizing the genetic diversity present in the germplasm bank of taro is fundamental to better manage, conserve and utilize the genetic resources of this species. In this study, the genetic diversity of 234 taro accessions from 16 provinces of China was assessed using 132,869 single nucleotide polymorphism (SNP) markers identified by specific length amplified fragment-sequencing (SLAF-seq). Population structure and principal component analysis permitted the accessions to be categorized into eight groups. The genetic diversity and population differentiation of the eight groups were evaluated using the characterized SNPs. Analysis of molecular variance showed that the variation among eight inferred groups was higher than that within groups, while a relatively small variance was found among the two morphological types and 16 collection regions. Further, a core germplasm set comprising 41 taro accessions that maintained the genetic diversity of the entire collection was developed based on the genotype. This research is expected to be valuable for genetic characterization, germplasm conservation, and breeding of taro.
Collapse
Affiliation(s)
- Zhixin Wang
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yalin Sun
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xinfang Huang
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Feng Li
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yuping Liu
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Honglian Zhu
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Zhengwei Liu
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Weidong Ke
- Wuhan Academy of Agricultural Sciences, Wuhan, Hubei, China
| |
Collapse
|
10
|
Wang H, Yan A, Sun L, Zhang G, Wang X, Ren J, Xu H. Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape. BMC PLANT BIOLOGY 2020; 20:411. [PMID: 32883214 PMCID: PMC7470616 DOI: 10.1186/s12870-020-02630-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/30/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, the information about their genetic mechanisms is limited, which results in low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits. RESULTS In the present work, a final integrated map consisting of 3411 SLAF markers on 19 linkage groups (LGs) with an average distance of 0.98 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. A total of 9 significant stable QTLs for Muscat flavor, berry firmness and berry shape were identified on two linkage groups among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new stable QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes (VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350) related to berry firmness and 3 genes (VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200) linked to berry shape were highlighted. Overexpression of VIT_08s0032g01110 in transgenic Arabidopsis plants caused the change of pod shape. CONCLUSIONS A new high-density genetic map with total 3411 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine. VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350 were found to be related to berry firmness, while VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200 were linked to berry shape.
Collapse
Affiliation(s)
- Huiling Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Beijing, 100093, P.R. China
| | - Ailing Yan
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
- Beijing Engineering Research Center for Deciduous Fruit Trees, Beijing, 100093, P.R. China
| | - Lei Sun
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Guojun Zhang
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Xiaoyue Wang
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Jiancheng Ren
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China
| | - Haiying Xu
- Beijing Academy of Forestry and Pomology Sciences, Beijing, 100093, China.
| |
Collapse
|
11
|
Lou L, Su X, Liu X, Liu Z. Construction of a high-density genetic linkage map and identification of gene controlling resistance to cucumber mosaic virus in Luffa cylindrica (L.) Roem. based on specific length amplified fragment sequencing. Mol Biol Rep 2020; 47:5831-5841. [PMID: 32700128 DOI: 10.1007/s11033-020-05652-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 07/08/2020] [Indexed: 10/23/2022]
Abstract
Luffa cylindrica L. is a cash crop which has important health, medicinal and industrial value, but no high saturation genetic map has been constructed owing to a lack of efficient markers. Furthermore, no genes were reportedly responsible for CMV resistance in Luffa spp. Specific length amplified fragment sequencing (SLAF-seq) is a valuable tool for large-scale discovery of markers and genetic mapping. The present study reported the construction of a high-density genetic map and the mapping of CMV resistant genes by using an F2 population of 130 individuals and their two inbred line parents. A total of 271.01 Mb pair-end reads were generated. 100,077 high-quality SLAFs were detected, and 7404 of them were polymorphic. Finally, 3701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1518.56 cM with an average distance of 0.41 cM between adjacent markers. Based on the newly constructed high-density map, one gene located on chromosome 1 (100.072-100.457 cM) was identified to regulate CMV resistance in L. cylindrica. A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica. The high-density genetic map and the CMV resistant gene mapped and predicted in this study will be useful in future research.
Collapse
Affiliation(s)
- Lina Lou
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China.
| | - Xiaojun Su
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| | - Xiaohong Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| | - Zhe Liu
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences/Laboratory for Horticultural Crop Genetic Improvement, Zhongling Street 50, Nanjing, 210014, Jiangsu Province, China
| |
Collapse
|
12
|
Fang H, Liu H, Ma R, Liu Y, Li J, Yu X, Zhang H, Yang Y, Zhang G. Genome-wide assessment of population structure and genetic diversity of Chinese Lou onion using specific length amplified fragment (SLAF) sequencing. PLoS One 2020; 15:e0231753. [PMID: 32369481 PMCID: PMC7199963 DOI: 10.1371/journal.pone.0231753] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/30/2020] [Indexed: 11/24/2022] Open
Abstract
Lou onion (Allium fistulosum L. var. viviparum) is an abundant source of flavonols which provides additional health benefits to diseases. Genome-wide specific length amplified fragment (SLAF) sequencing method is a rapidly developed deep sequencing technologies used for selection and identification of genetic loci or markers. This study aimed to elucidate the genetic diversity of 122 onion accessions in China using the SLAF-seq method. A set of 122 onion accessions including 107 A.fistulosum L. var. viviparum Makino, 3 A.fistulosum L. var. gigantum Makino, 3 A.mongolicum Regel and 9 A.cepa L. accessions (3 whites, 3 reds and 3 yellows) from different regions in China were enrolled. Genomic DNA was isolated from young leaves and prepared for the SLAF-seq, which generated a total of 1,387.55 M reads and 162,321 high quality SNPs (integrity >0.5 and MAF >0.05). These SNPs were used for the construction of neighbor-joining phylogenetic tree, in which 10 A.fistulosum L. var. viviparum Makino accessions from Yinchuan (Ningxia province) and Datong (Qinghai province) had close genetic relationship. The 3 A.cepa L. clusters (red, white and yellow) had close genetic relationship especially with the 97 A.fistulosum L. var. viviparum Makino accessions. Population structure analysis suggested entire population could be clustered into 3 groups, while principal component analysis (PCA) showed there were 4 genetic groups. We confirmed the SLAF-seq approach was effective in genetic diversity analysis in red onion accessions. The key findings would provide a reference to the Lou onion germplasm in China.
Collapse
Affiliation(s)
- Haitian Fang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
- * E-mail: (HF); (GZ)
| | - Huiyan Liu
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Ruoshuang Ma
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Yuxuan Liu
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Jinna Li
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Xiaoyan Yu
- Technological Innovation Center of Protected Horticulture (Ningxia University) in Ningxia, Yinchuan, China
- Technological Innovation center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, China
| | - Haoyu Zhang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Yali Yang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
| | - Guangdi Zhang
- School of Agriculture, Ningxia University, Yinchuan, China
- Ningxia Key Laboratory for Food Microbial-Applications Technology and Safety Control, Ningxia University, Yinchuan, China
- Technological Innovation Center of Protected Horticulture (Ningxia University) in Ningxia, Yinchuan, China
- Technological Innovation center of Horticulture (Ningxia University), Ningxia Hui Autonomous Region, Yinchuan, China
- * E-mail: (HF); (GZ)
| |
Collapse
|
13
|
Wang F, Zhang J, Chen Y, Zhang C, Gong J, Song Z, Zhou J, Wang J, Zhao C, Jiao M, Liu A, Du Z, Yuan Y, Fan S, Zhang J. Identification of candidate genes for key fibre-related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:707-720. [PMID: 31446669 PMCID: PMC7004909 DOI: 10.1111/pbi.13237] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 08/15/2019] [Indexed: 05/02/2023]
Abstract
Fine mapping QTLs and identifying candidate genes for cotton fibre-quality and yield traits would be beneficial to cotton breeding. Here, we constructed a high-density genetic map by specific-locus amplified fragment sequencing (SLAF-seq) to identify QTLs associated with fibre-quality and yield traits using 239 recombinant inbred lines (RILs), which was developed from LMY22 (a high-yield Gossypium hirsutumL. cultivar) × LY343 (a superior fibre-quality germplasm with G. barbadenseL. introgressions). The genetic map spanned 3426.57 cM, including 3556 SLAF-based SNPs and 199 SSR marker loci. A total of 104 QTLs, including 67 QTLs for fibre quality and 37 QTLs for yield traits, were identified with phenotypic data collected from 7 environments. Among these, 66 QTLs were co-located in 19 QTL clusters on 12 chromosomes, and 24 QTLs were detected in three or more environments and determined to be stable. We also investigated the genomic components of LY343 and their contributions to fibre-related traits by deep sequencing the whole genome of LY343, and we found that genomic components from G. hirsutum races (which entered LY343 via its G. barbadense parent) contributed more favourable alleles than those from G. barbadense. We further identified six putative candidate genes for stable QTLs, including Gh_A03G1147 (GhPEL6), Gh_D07G1598 (GhCSLC6) and Gh_D13G1921 (GhTBL5) for fibre-length QTLs and Gh_D03G0919 (GhCOBL4), Gh_D09G1659 (GhMYB4) and Gh_D09G1690 (GhMYB85) for lint-percentage QTLs. Our results provide comprehensive insight into the genetic basis of the formation of fibre-related traits and would be helpful for cloning fibre-development-related genes as well as for marker-assisted genetic improvement in cotton.
Collapse
Affiliation(s)
- Furong Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jingxia Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Yu Chen
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chuanyun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juwu Gong
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhangqiang Song
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Juan Zhou
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Jingjing Wang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Chengjie Zhao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Mengjia Jiao
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Aiying Liu
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Zhaohai Du
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
| | - Youlu Yuan
- State Key Laboratory of Cotton BiologyKey Laboratory of Biological and Genetic Breeding of CottonMinistry of AgricultureInstitute of Cotton ResearchChinese Academy of Agricultural SciencesAnyangChina
| | - Shoujin Fan
- College of Life SciencesShandong Normal UniversityJinanChina
| | - Jun Zhang
- Key Laboratory of Cotton Breeding and Cultivation in Huang‐Huai‐Hai PlainMinistry of AgricultureCotton Research Center of Shandong Academy of Agricultural SciencesJinanChina
- College of Life SciencesShandong Normal UniversityJinanChina
| |
Collapse
|
14
|
Xu X, Pan J, He M, Tian H, Qi X, Xu Q, Chen X. Transcriptome profiling reveals key genes related to astringency during cucumber fruit development. 3 Biotech 2019; 9:390. [PMID: 31656728 DOI: 10.1007/s13205-019-1922-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 09/25/2019] [Indexed: 12/31/2022] Open
Abstract
The goal of this study was to provide quantitative data on the catechin contents and underlying molecular regulatory mechanisms in cucumber during fruit development. The dynamic changes in the total catechin contents and RNA-seq-based transcriptome profiling of the flesh and peel of the cucumber cultivar 'YanBai', which is strongly astringent, were examined at three key developmental stages 3, 6 and 9 days post-pollination. The total catechin content decreased as cucumber fruit developed and was significantly lower in the flesh than in the peel. In total, 5092 and 4004 genes were found to be differently expressed in the peel and flesh, respectively. Based on a functional annotation, eight structural genes encode enzymes involved in the catechin biosynthesis pathway. Three genes encoding 4-coumarate-CoA ligases, two genes encoding chalcone isomerases, two genes encoding dihydroflavonol-4-reductase and one gene each encoding a phenylalanine ammonia-lyase, flavanone 3-hydroxylase and cinnamate 4-hydroxylase were identified as affecting the catechin content of cucumber. The transcriptome data also revealed the significance of transcription factors, including WD40-repeat proteins, MYB and bHLH, in regulating catechin biosynthesis. These findings help increase our understanding of the molecular mechanisms controlling catechin biosynthesis and astringency development in cucumber fruit.
Collapse
Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Jiawei Pan
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Min He
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Henglu Tian
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, 225009 Jiangsu China
| |
Collapse
|
15
|
Yang M, Li G, Wan H, Li L, Li J, Yang W, Pu Z, Yang Z, Yang E. Identification of QTLs for Stripe Rust Resistance in a Recombinant Inbred Line Population. Int J Mol Sci 2019; 20:ijms20143410. [PMID: 31336736 PMCID: PMC6678735 DOI: 10.3390/ijms20143410] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 12/02/2022] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating fungal diseases of wheat worldwide. It is essential to discover more sources of stripe rust resistance genes for wheat breeding programs. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for the construction of high-density genetic maps. In this study, a set of 200 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Chuanmai 42 (CH42) and Chuanmai 55 (CH55) was used to construct a high-density genetic map and to identify quantitative trait loci (QTLs) for stripe rust resistance using SLAF-seq technology. A genetic map of 2828.51 cM, including 21 linkage groups, contained 6732 single nucleotide polymorphism markers (SNP). Resistance QTLs were identified on chromosomes 1B, 2A, and 7B; Qyr.saas-7B was derived from CH42, whereas Qyr.saas-1B and Qyr.saas-2A were from CH55. The physical location of Qyr.saas-1B, which explained 6.24–34.22% of the phenotypic variation, overlapped with the resistance gene Yr29. Qyr.saas-7B accounted for up to 20.64% of the phenotypic variation. Qyr.saas-2A, a minor QTL, was found to be a likely new stripe rust resistance locus. A significant additive effect was observed when all three QTLs were combined. The combined resistance genes could be of value in breeding wheat for stripe rust resistance.
Collapse
Affiliation(s)
- Manyu Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Guangrong Li
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Hongshen Wan
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Liping Li
- Chengdu Academy of Agricultural and Forestry Sciences, Wenjiang, Chengdu 611130, China
| | - Jun Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Wuyun Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Zongjun Pu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
| | - Ennian Yang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China.
| |
Collapse
|
16
|
Li GH, Chen HC, Liu JL, Luo WL, Xie DS, Luo SB, Wu TQ, Akram W, Zhong YJ. A high-density genetic map developed by specific-locus amplified fragment (SLAF) sequencing and identification of a locus controlling anthocyanin pigmentation in stalk of Zicaitai (Brassica rapa L. ssp. chinensis var. purpurea). BMC Genomics 2019; 20:343. [PMID: 31064320 PMCID: PMC6503552 DOI: 10.1186/s12864-019-5693-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study is to construct a high density genetic map using the specific length amplified fragment sequencing (SLAF-seq) technique to explore genetic basis for anthocyanin pigmentation traits via quantitative trait loci (QTL) mapping. RESULTS We constructed a high generation linkage map with a mapping panel of F2 populations derived from 150 individuals of parental lines "Xianghongtai 01" and "Yinong 50D" with purple and green stalk respectively. The map was constructed containing 4253 loci, representing 10,940 single nucleotide polymorphism (SNP) markers spanning 1030.04 centiMorgans (cM) over 10 linkage groups (LGs), with an average distance between markers of 0.27 cM. Quantitative trait loci (QTL) analysis revealed that a major locus on chromosome 7 and 4 minor QTLs explaining 2.69-61.21% of phenotypic variation (PVE) were strongly responsible for variation in stalk color trait. Bioinformatics analysis of the major locus identified 62 protein-coding genes. Among the major locus, there were no biosynthetic genes related to anthocyanin. However, there were several transcription factors like helix-loop-helix (bHLH) bHLH, MYB in the locus. Seven predicted candidate genes were selected for the transcription level analysis. Only bHLH49 transcription factor, was significantly higher expressed in both stalks and young leaves of Xianghongtai01 than Yinong50D. An insertion and deletion (InDel) marker developed from deletion/insertion in the promoter region of bHLH49 showed significant correlation with the stalk color trait in the F2 population. CONCLUSION Using the constructed high-qualified linkage map, this study successfully identified QTLs for stalk color trait. The identified valuable markers and candidate genes for anthocyanin accumulation in stalk will provide useful information for molecular regulation of anthocyanin biosynthesis. Overall our findings will lay a foundation for functional gene cloning, marker-assisted selection (MAS) and molecular breeding of important economic traits in B. rapa.
Collapse
Affiliation(s)
- Gui-Hua Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Han-Cai Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Jia-Li Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Wen-Long Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Da-Sen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Shao-Bo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Ting-Quan Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Waheed Akram
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Yu-Juan Zhong
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China. .,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China.
| |
Collapse
|
17
|
Du X, Zhang X, Bu H, Zhang T, Lao Y, Dong W. Molecular Analysis of Evolution and Origins of Cultivated Hawthorn ( Crataegus spp.) and Related Species in China. FRONTIERS IN PLANT SCIENCE 2019; 10:443. [PMID: 31024604 PMCID: PMC6465762 DOI: 10.3389/fpls.2019.00443] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Hawthorn is of high economic value owing to its medicinal properties and health benefits. Crataegus is a member of the Rosaceae family; the genus has a complicated taxonomic history, and several theories on its origin have been proposed. In this study, 53 accessions from seven Crataegus taxa native to China and accessions of exotic Crataegus species (two from Europe and one from North America) were analyzed by specific locus amplified fragment sequencing (SLAF-seq). In total, 933,450 single-nucleotide polymorphisms were identified after filtering and used to investigate the species' genomic evolution. Phylogenetic trees derived from nuclear simple sequence repeats (SSRs) and SLAF-seq data showed the same topology, in which Crataegus maximowiczii and Crataegus sanguineae formed a closely related cluster that was clearly separated from the cluster composed of Crataegus hupehensis, Crataegus pinnatifida, Crataegus pinnatifida var. major, Crataegus bretschneideri and Crataegus scabrifolia. Phylogenetic and structure analysis indicated that the seven Chinese Crataegus taxa had two separate speciation events. Plants that evolved the southwestern route shared the genepool with the European species, whereas plants along the northeastern route shared the genepool with the North American species. TreeMix genetic analysis revealed that C. bretschneideri may have a hybrid origin. This study provides valuable information on the origins of Chinese Crataegus and suggests an evolutionary model for the main Crataegus species that native to China.
Collapse
Affiliation(s)
- Xiao Du
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Xiao Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Haidong Bu
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
- Mudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang, China
| | - Ticao Zhang
- College of Chinese Material Medica, Yunnan University of Traditional Chinese Medicine, Kunming, China
| | - Yongchun Lao
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Wenxuan Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, China
| |
Collapse
|
18
|
Waiho K, Shi X, Fazhan H, Li S, Zhang Y, Zheng H, Liu W, Fang S, Ikhwanuddin M, Ma H. High-Density Genetic Linkage Maps Provide Novel Insights Into ZW/ZZ Sex Determination System and Growth Performance in Mud Crab ( Scylla paramamosain). Front Genet 2019; 10:298. [PMID: 31024620 PMCID: PMC6459939 DOI: 10.3389/fgene.2019.00298] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 03/19/2019] [Indexed: 02/06/2023] Open
Abstract
Mud crab, Scylla paramamosain is one of the most important crustacean species in global aquaculture. To determine the genetic basis of sex and growth-related traits in S. paramamosain, a high-density genetic linkage map with 16,701 single nucleotide polymorphisms (SNPs) was constructed using SLAF-seq and a full-sib family. The consensus map has 49 linkage groups, spanning 5,996.66 cM with an average marker-interval of 0.81 cM. A total of 516 SNP markers, including 8 female-specific SNPs segregated in two quantitative trait loci (QTLs) for phenotypic sex were located on LG32. The presence of female-specific SNP markers only on female linkage map, their segregation patterns and lower female: male recombination rate strongly suggest the conformation of a ZW/ZZ sex determination system in S. paramamosain. The QTLs of most (90%) growth-related traits were found within a small interval (25.18–33.74 cM) on LG46, highlighting the potential involvement of LG46 in growth. Four markers on LG46 were significantly associated with 10–16 growth-related traits. BW was only associated with marker 3846. Based on the annotation of transcriptome data, 11 and 2 candidate genes were identified within the QTL regions of sex and growth-related traits, respectively. The newly constructed high-density genetic linkage map with sex-specific SNPs, and the identified QTLs of sex- and growth-related traits serve as a valuable genetic resource and solid foundation for marker-assisted selection and genetic improvement of crustaceans.
Collapse
Affiliation(s)
- Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Xi Shi
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Shaobin Fang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, Kuala Terengganu, Malaysia
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, China.,STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| |
Collapse
|
19
|
Wang Y, Wang C, Han H, Luo Y, Wang Z, Yan C, Xu W, Qu S. Construction of a High-Density Genetic Map and Analysis of Seed-Related Traits Using Specific Length Amplified Fragment Sequencing for Cucurbita maxima. FRONTIERS IN PLANT SCIENCE 2019; 10:1782. [PMID: 32153597 PMCID: PMC7046561 DOI: 10.3389/fpls.2019.01782] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 12/20/2019] [Indexed: 05/03/2023]
Abstract
Seed traits are agronomically important for Cucurbita breeding, but the genes controlling seed size, seed weight and seed number have not been mapped in Cucurbita maxima (C. maxima). In this study, 100 F2 individual derived from two parental lines, "2013-12" and "9-6", were applied to construct a 3,376.87-cM genetic map containing 20 linkage groups (LGs) with an average genetic distance of 0.47 cM using a total of 8,406 specific length amplified fragment (SLAF) markers in C. maxima. Ten quantitative trait loci (QTLs) of seed width (SW), seed length (SL) and hundred-seed weight (HSW) were identified using the composite interval mapping (CIM) method. The QTLs affecting SW, SL and HSW explained a maximum of 38.6%, 28.9% and 17.2% of the phenotypic variation and were detected in LG6, LG6 and LG17, respectively. To validate these results, an additional 150 F2 individuals were used for QTL mapping of SW and SL with cleaved amplified polymorphic sequence (CAPS) markers. We found that two major QTLs, SL6-1 and SW6-1, could be detected in both SLAF-seq and CAPS markers in an overlapped region. Based on gene annotation and non-synonymous single-nucleotide polymorphisms (SNPs) in the major SWand SL-associated regions, we found that two genes encoding a VQ motif and an E3 ubiquitin-protein ligase may be candidate genes influencing SL, while an F-box and leucinerich repeat (LRR) domain-containing protein is the potential regulator for SW in C. maxima. This study provides the first high-density linkage map of C. maxima using SNPs developed by SLAF-seq technology, which is a powerful tool for associated mapping of important agronomic traits, map-based gene cloning and marker-assisted selection (MAS)-based breeding in C. maxima.
Collapse
Affiliation(s)
- Yunli Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Chaojie Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Hongyu Han
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Yusong Luo
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Zhichao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Chundong Yan
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Wenlong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Shuping Qu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs/Northeast Agricultural University, Harbin, China
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- *Correspondence: Shuping Qu,
| |
Collapse
|
20
|
Li L, Yang X, Cui S, Meng X, Mu G, Hou M, He M, Zhang H, Liu L, Chen CY. Construction of High-Density Genetic Map and Mapping Quantitative Trait Loci for Growth Habit-Related Traits of Peanut ( Arachis hypogaea L.). FRONTIERS IN PLANT SCIENCE 2019; 10:745. [PMID: 31263472 PMCID: PMC6584813 DOI: 10.3389/fpls.2019.00745] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/20/2019] [Indexed: 05/03/2023]
Abstract
Plant growth habit is an important and complex agronomic trait and is associated with yield, disease resistance, and mechanized harvesting in peanuts. There are at least two distinct growth habits (erect and prostrate) and several intermediate forms existing in the peanut germplasm. A recombinant inbred line population containing 188 individuals was developed from a cross of "Jihua 5" and "M130" for genetically dissecting the architecture of the growth habit. A new high-density genetic linkage map was constructed by using specific locus amplified fragment sequencing technology. The map contains 2,808 single-nucleotide polymorphism markers distributed on 20 linkage groups with a total length of 1,308.20 cM and an average inter-marker distance of 0.47 cM. The quantitative trait locus (QTL) analysis of the growth habit-related traits was conducted based on phenotyping data from seven environments. A total of 39 QTLs for growth habit-related traits was detected on 10 chromosomes explaining 4.55-27.74% of the phenotypic variance, in which 6 QTLs were for lateral branch angle, 8 QTLs were for extent radius, 7 QTLs were for the index of plant type, 11 QTLs were for main stem height, and 7 QTLs were for lateral branch length. Among these QTLs, 12 were co-localized on chromosome B05 spanning an approximately 0.17 Mb physical interval in comparison with the allotetraploid reference genome of "Tifrunner." Analysis of the co-localized genome region has shown that the putative genes are involved in light and hormones and will facilitate peanut growth habit molecular breeding and study of peanut domestication.
Collapse
Affiliation(s)
- Li Li
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Xinlei Yang
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Shunli Cui
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinhao Meng
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Guojun Mu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Mingyu Hou
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Meijing He
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Hui Zhang
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
| | - Lifeng Liu
- North China Key Laboratory for Crop Germplasm Resources of Education Ministry, College of Agronomy, Hebei Agricultural University, Baoding, China
- *Correspondence: Lifeng Liu,
| | - Charles Y. Chen
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, United States
- Charles Y. Chen,
| |
Collapse
|
21
|
Zhou F, Liu Y, Liang C, Wang W, Li C, Guo Y, Ma J, Yu Y, Fan L, Yao Y, Zhao D, Liu X, Huang X. Construction of a high-density genetic linkage map and QTL mapping of oleic acid content and three agronomic traits in sunflower ( Helianthus annuus L.) using specific-locus amplified fragment sequencing (SLAF-seq). BREEDING SCIENCE 2018; 68:596-605. [PMID: 30697121 PMCID: PMC6345229 DOI: 10.1270/jsbbs.18051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/18/2018] [Indexed: 05/19/2023]
Abstract
High-density genetic linkage maps are particularly important for quantitative trait loci (QTL) mapping, genome assembly, and marker-assisted selection (MAS) in plants. In this study, a high-density genetic linkage map of sunflower (Helianthus annuus L.) was constructed using an F2 population generated from a cross between Helianthus annuus L. '86-1' and 'L-1-OL-1' via specific-locus amplified fragment sequencing (SLAF-seq). After sequence preprocessing, 530.50 M reads (105.60 Gb) were obtained that contained a total of 343,197 SLAFs, of which 39,589 were polymorphic. Of the polymorphic SLAFs, 6,136 were organized into a linkage map consisting of 17 linkage groups (LGs) spanning 2,221.86 cM, with an average genetic distance of 0.36 cM between SLAFs. Based on this high-density genetic map, QTL analysis was performed that focused on four sunflower phenotypic traits: oleic acid content (OAC), plant height (PH), head diameter (HD), and stem diameter (SD). Subsequently, for these four traits eight QTLs were detected that will likely be useful for increasing our understanding of genetic factors underlying these traits and for use in marker-assisted selection (MAS) for future sunflower breeding.
Collapse
Affiliation(s)
- Fei Zhou
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yan Liu
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Chunbo Liang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Wenjun Wang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Cen Li
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yongli Guo
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Jun Ma
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Ying Yu
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Lijuan Fan
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Yubo Yao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Dongsheng Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
| | - Xuemei Liu
- College of Life Science, Northeast Forestry University,
Harbin, 150040,
China
| | - Xutang Huang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences,
Harbin, 150086,
China
- Corresponding author (e-mail: )
| |
Collapse
|
22
|
Li F, Han H, Lei Q, Gao J, Liu J, Liu W, Zhou Y, Li H, Cao D. Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology. J Appl Genet 2018; 59:305-312. [PMID: 29946990 DOI: 10.1007/s13353-018-0452-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022]
Abstract
Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (PRSS23, ME3, FAM181B, NABP1, SDPR, TSSK6L2, and RBBP8). Moreover, 24 BW-associated SNPs reached "suggestive" genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.
Collapse
Affiliation(s)
- Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Huimin Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China. .,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China.
| |
Collapse
|
23
|
Fan L, Wang L, Wang X, Zhang H, Zhu Y, Guo J, Gao W, Geng H, Chen Q, Qu Y. A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by-sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population. BMC Genomics 2018; 19:489. [PMID: 29940861 PMCID: PMC6019718 DOI: 10.1186/s12864-018-4890-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 06/19/2018] [Indexed: 01/08/2023] Open
Abstract
Background Gossypium barbadense (Sea Island, Egyptian or Pima cotton) cotton has high fiber quality, however, few studies have investigated the genetic basis of its traits using molecular markers. Genome complexity reduction approaches such as genotyping-by-sequencing have been utilized to develop abundant markers for the construction of high-density genetic maps to locate quantitative trait loci (QTLs). Results The Chinese G. barbadense cultivar 5917 and American Pima S-7 were used to develop a recombinant inbred line (RIL) population with 143 lines. The 143 RILs together with their parents were tested in three replicated field tests for lint yield traits (boll weight and lint percentage) and fiber quality traits (fiber length, fiber elongation, fiber strength, fiber uniformity and micronaire) and then genotyped using GBS to develop single-nucleotide polymorphism (SNP) markers. A high-density genetic map with 26 linkage groups (LGs) was constructed using 3557 GBS SNPs spanning a total genetic distance of 3076.23 cM at an average density of 1.09 cM between adjacent markers. A total of 42 QTLs were identified, including 24 QTLs on 12 LGs for fiber quality and 18 QTLs on 7 LGs for lint yield traits, with LG1 (9 QTLs), LG10 (7 QTLs) and LG14 (6 QTLs) carrying more QTLs. Common QTLs for the same traits and overlapping QTLs for different traits were detected. Each individual QTLs explained 0.97 to 20.7% of the phenotypic variation. Conclusions This study represents one of the first genetic mapping studies on the fiber quality and lint yield traits in a RIL population of G. barbadense using GBS-SNPs. The results provide important information for the subsequent fine mapping of QTLs and the prediction of candidate genes towards map-based cloning and marker-assisted selection in cotton.
Collapse
Affiliation(s)
- Liping Fan
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Liping Wang
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Xinyi Wang
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Haiyan Zhang
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Yanfei Zhu
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Jiayan Guo
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Wenwei Gao
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Hongwei Geng
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Quanjia Chen
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China
| | - Yanying Qu
- Department of Agronomy, Key Laboratory of Agriculture Biological Technology, Xinjiang Agriculture University, Urumqi, 830052, China.
| |
Collapse
|
24
|
Hu XH, Zhang SZ, Miao HR, Cui FG, Shen Y, Yang WQ, Xu TT, Chen N, Chi XY, Zhang ZM, Chen J. High-Density Genetic Map Construction and Identification of QTLs Controlling Oleic and Linoleic Acid in Peanut using SLAF-seq and SSRs. Sci Rep 2018; 8:5479. [PMID: 29615772 PMCID: PMC5883025 DOI: 10.1038/s41598-018-23873-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 03/20/2018] [Indexed: 11/08/2022] Open
Abstract
The cultivated peanut, A. hypogaea L., is an important oil and food crop globally.High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this context, a recombinant inbred line (RIL) of 146 lines was developed by crossing Huayu28 and P76. We developed 433,679 high-quality SLAFs, of which 29,075 were polymorphic. 4,817 SLAFs were encoded and grouped into different segregation patterns. A high-resolution genetic map containing 2,334 markers (68 SSRs and 2,266 SNPs) on 20 linkage groups (LGs) spanning 2586.37 cM was constructed for peanut. The average distance between adjacent markers was 2.25 cM. Based on phenotyping in seven environments, QTLs for oleic acid (C18:1), linoleic acid (C18:2) and the ratio of oleic acid to linoleic acid (O/L) were identified and positioned on linkage groups A03, A04, A09, B09 and B10. Marker2575339 and Marker2379598 in B09 were associated with C18:1, C18:2 and O/L in seven environments, Marker4391589 and Marker4463600 in A09 were associated with C18:1, C18:2 and O/L in six environments. This map exhibits high resolution and accuracy, which will facilitate QTL discovery for essential agronomic traits in peanut.
Collapse
Affiliation(s)
- X H Hu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - S Z Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - H R Miao
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - F G Cui
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Y Shen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, P.R. China
| | - W Q Yang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - T T Xu
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - N Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - X Y Chi
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - Z M Zhang
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China
| | - J Chen
- Shandong Peanut Research Institute, Qingdao, 266100, P.R. China.
| |
Collapse
|
25
|
Wang Y, VandenLangenberg K, Wen C, Wehner TC, Weng Y. QTL mapping of downy and powdery mildew resistances in PI 197088 cucumber with genotyping-by-sequencing in RIL population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:597-611. [PMID: 29159421 DOI: 10.1007/s00122-017-3022-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 11/10/2017] [Indexed: 05/02/2023]
Abstract
Host resistances in PI 197088 cucumber to downy and powdery mildew pathogens are conferred by 11 (3 with major effect) and 4 (1 major effect) QTL, respectively, and three of which are co-localized. The downy mildew (DM) and powdery mildew (PM) are the two most important foliar diseases of cucurbit crops worldwide. The cucumber accession PI 197088 exhibits high-level resistances to both pathogens. Here, we reported QTL mapping results for DM and PM resistances with 148 recombinant inbred lines from a cross between PI 197088 and the susceptible line 'Coolgreen'. Phenotypic data on responses to natural DM and PM infection were collected in multi-year and multi-location replicated field trials. A high-density genetic map with 2780 single nucleotide polymorphisms (SNPs) from genotyping-by-sequencing and 55 microsatellite markers was developed, which revealed genomic regions with segregation distortion and mis-assemblies in the '9930' cucumber draft genome. QTL analysis identified 11 and 4 QTL for DM and PM resistances accounting for more than 73.5 and 63.0% total phenotypic variance, respectively. Among the 11 DM resistance QTL, dm5.1, dm5.2, and dm5.3 were major-effect contributing QTL, whereas dm1.1, dm2.1, and dm6.2 conferred susceptibility. Of the 4 QTL for PM resistance, pm5.1 was the major-effect QTL explaining 32.4% phenotypic variance and the minor-effect QTL pm6.1 contributed to disease susceptibility. Three PM QTL, pm2.1, pm5.1, and pm6.1, were co-localized with DM QTL dm2.1, dm5.2, and dm6.1, respectively, which was consistent with the observed linkage of PM and DM resistances in PI 197088. The genetic architecture of DM resistance in PI 197088 and another resistant line WI7120 (PI 330628) was compared, and the potential of using PI 197088 in cucumber breeding for downy and powdery mildew resistances is discussed.
Collapse
Affiliation(s)
- Yuhui Wang
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Kyle VandenLangenberg
- Horticultural Science Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Changlong Wen
- Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Todd C Wehner
- Horticultural Science Department, North Carolina State University, Raleigh, NC, 27695, USA
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA.
- USDA-ARS Vegetable Crops Research Unit, Madison, WI, 53705, USA.
| |
Collapse
|
26
|
Li N, Yin Y, Wang F, Yao M. Construction of a high-density genetic map and identification of QTLs for cucumber mosaic virus resistance in pepper ( Capsicum annuum L.) using specific length amplified fragment sequencing (SLAF-seq). BREEDING SCIENCE 2018; 68:233-241. [PMID: 29875607 PMCID: PMC5982177 DOI: 10.1270/jsbbs.17063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/13/2017] [Indexed: 05/09/2023]
Abstract
Pepper (Capsicum) is one of the most important vegetable and spice crops. Aphid-transmitted cucumber mosaic virus (CMV) causes significant damage to pepper crops across the world. The genetic basis of CMV resistance in pepper is complex, and the mechanisms underlying resistance remain largely unknown. Here, we employed a SLAF-seq approach to generate a high-density genetic map of pepper. The map spanned 1,785.46 cM, containing 12,727 markers on 12 chromosomes, with a mean marker distance of 0.16 cM between adjacent markers. We used this map and the interval mapping (IM) and multiple QTL mapping (MQM) procedures to detect genetic regions associated with quantitative trait for CMV resistance. Three QTLs, qcmv11.1, qcmv11.2 and qcmv12.1, conferred resistance to CMV and showed trait variation of 10.2%, 19.2% and 7.3% respectively. Our results will help to develop markers linked to CMV-resistant QTLs to improve pepper resistance to CMV.
Collapse
Affiliation(s)
| | | | - Fei Wang
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences,
Wuhan 430064,
China
| | - Minghua Yao
- Cash Crops Research Institute, Hubei Academy of Agricultural Sciences,
Wuhan 430064,
China
| |
Collapse
|
27
|
Wu J, Zhao Q, Zhang L, Li S, Ma Y, Pan L, Lin H, Wu G, Yuan H, Yu Y, Wang X, Yang X, Li Z, Jiang T, Sun D. QTL Mapping of Fiber-Related Traits Based on a High-Density Genetic Map in Flax ( Linum usitatissimum L.). FRONTIERS IN PLANT SCIENCE 2018; 9:885. [PMID: 30065730 PMCID: PMC6056681 DOI: 10.3389/fpls.2018.00885] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 06/07/2018] [Indexed: 05/18/2023]
Abstract
UNLABELLED A genetic map is an important and valuable tool for quantitative trait locus (QTL) mapping, marker-assisted selection (MAS)-based breeding, and reference-assisted chromosome assembly. In this study, 112 F2 plants from a cross between Linum usitatissimum L. "DIANE" and "NY17" and parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 61.64 Gb of raw data containing 253.71 Mb paired-end reads, each 101 bp in length, were obtained. A total of 192,797 SLAFs were identified, of which 23,115 were polymorphic, with a polymorphism rate of 11.99%. Finally, 2,339 SLAFs were organized into a linkage map consisting of 15 linkage groups (LGs). The total length of the genetic map was 1483.25 centimorgans (cM) and the average distance between adjacent markers was 0.63 cM. Combined with flax chromosome-scale pseudomolecules, 12 QTLs associating with 6 flax fiber-related traits were mapped on the chromosomal scaffolds. This high-density genetic map of flax should serve as a foundation for flax fine QTL mapping, draft genome assembly, and MAS-guided breeding. Ultimately, the genomic regions identified in this research could potentially be valuable for improving flax fiber cultivars, as well as for identification of candidate genes involved in flax fiber formation processes. SIGNIFICANCE STATEMENT A high-density genetic map of flax was constructed, and QTLs were identified on the sequence scaffolds to be interrelated with fiber-related traits. The results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for flax, but also provide a reference to help position sequence scaffolds on the physical map and assist in the process of assembling the flax genome sequence.
Collapse
Affiliation(s)
- Jianzhong Wu
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Qian Zhao
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liyan Zhang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Suiyan Li
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yanhua Ma
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liyan Pan
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hong Lin
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Guangwen Wu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Hongmei Yuan
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Ying Yu
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xun Wang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xue Yang
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhugang Li
- Heilongjiang Academy of Agricultural Sciences, Harbin, China
- *Correspondence: Zhugang Li
| | - Tingbo Jiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Tingbo Jiang
| | - Dequan Sun
- Institute of Forage and Grassland Sciences, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- Dequan Sun
| |
Collapse
|
28
|
Yi L, Gao F, Siqin B, Zhou Y, Li Q, Zhao X, Jia X, Zhang H. Construction of an SNP-based high-density linkage map for flax (Linum usitatissimum L.) using specific length amplified fragment sequencing (SLAF-seq) technology. PLoS One 2017; 12:e0189785. [PMID: 29267332 PMCID: PMC5739455 DOI: 10.1371/journal.pone.0189785] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Flax is an important crop for oil and fiber, however, no high-density genetic maps have been reported for this species. Specific length amplified fragment sequencing (SLAF-seq) is a high-resolution strategy for large scale de novo discovery and genotyping of single nucleotide polymorphisms. In this study, SLAF-seq was employed to develop SNP markers in an F2 population to construct a high-density genetic map for flax. In total, 196.29 million paired-end reads were obtained. The average sequencing depth was 25.08 in male parent, 32.17 in the female parent, and 9.64 in each F2 progeny. In total, 389,288 polymorphic SLAFs were detected, from which 260,380 polymorphic SNPs were developed. After filtering, 4,638 SNPs were found suitable for genetic map construction. The final genetic map included 4,145 SNP markers on 15 linkage groups and was 2,632.94 cM in length, with an average distance of 0.64 cM between adjacent markers. To our knowledge, this map is the densest SNP-based genetic map for flax. The SNP markers and genetic map reported in here will serve as a foundation for the fine mapping of quantitative trait loci (QTLs), map-based gene cloning and marker assisted selection (MAS) for flax.
Collapse
Affiliation(s)
- Liuxi Yi
- Biotechnology Research Center, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Fengyun Gao
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Bateer Siqin
- Biotechnology Research Center, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Yu Zhou
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Qiang Li
- Corn Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Xiaoqing Zhao
- Biotechnology Research Center, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Xiaoyun Jia
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| | - Hui Zhang
- Special Crops Institute, Inner Mongolia Academy of Agricultural and Husbandry Sciences, Hohhot, Inner Mongolia, China
| |
Collapse
|
29
|
Niu D, Du Y, Wang Z, Xie S, Nguyen H, Dong Z, Shen H, Li J. Construction of the First High-Density Genetic Linkage Map and Analysis of Quantitative Trait Loci for Growth-Related Traits in Sinonovacula constricta. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:488-496. [PMID: 28725940 DOI: 10.1007/s10126-017-9768-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/26/2017] [Indexed: 06/07/2023]
Abstract
The razor clam (Sinonovacula constricta) is an important aquaculture species, for which a high-density genetic linkage map would play an important role in marker-assisted selection (MAS). In this study, we constructed a high-density genetic map and detected quantitative trait loci (QTLs) for Sinonovacula constricta with an F1 cross population by using the specific locus amplified fragment sequencing (SLAF-seq) method. A total of 315,553 SLAF markers out of 467.71 Mreads were developed. The final linkage map was composed of 7516 SLAFs (156.60-fold in the parents and 20.80-fold in each F1 population on average). The total distance of the linkage map was 2383.85 cM, covering 19 linkage groups with an average inter-marker distance of 0.32 cM. The proportion of gaps less than 5.0 cM was on average 96.90%. A total of 16 suggestive QTLs for five growth-related traits (five QTLs for shell height, six QTLs for shell length, three QTLs for shell width, one QTL for total body weight, and one QTL for soft body weight) were identified. These QTLs were distributed on five linkage groups, and the regions showed overlapping on LG9 and LG13. In conclusion, the high-density genetic map and QTLs for S. constricta provide a valuable genetic resource and a basis for MAS.
Collapse
Affiliation(s)
- Donghong Niu
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
- National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Yunchao Du
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Ze Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Shumei Xie
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Haideng Nguyen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhiguo Dong
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China
| | - Heding Shen
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China
- Shanghai Engineering Research Center of Aquaculture, Shanghai, 201306, China
| | - Jiale Li
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, 201306, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang, 222005, China.
- College of Aquaculture and Life Science, Shanghai Ocean University, Shanghai, 201306, China.
| |
Collapse
|
30
|
Wang J, Su K, Guo Y, Xing H, Zhao Y, Liu Z, Li K, Guo X. Construction of a high-density genetic map for grape using specific length amplified fragment (SLAF) sequencing. PLoS One 2017; 12:e0181728. [PMID: 28746364 PMCID: PMC5528875 DOI: 10.1371/journal.pone.0181728] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/06/2017] [Indexed: 12/30/2022] Open
Abstract
Genetic maps are important tools in plant genomics and breeding. We report a large-scale discovery of single nucleotide polymorphisms (SNPs) using the specific length amplified fragment sequencing (SLAF-seq) technique for the construction of high-density genetic maps for two elite wine grape cultivars, ‘Chardonnay’ and ‘Beibinghong’, and their 130 F1 plants. A total of 372.53 M paired-end reads were obtained after preprocessing. The average sequencing depth was 33.81 for ‘Chardonnay’ (the female parent), 48.20 for ‘Beibinghong’ (the male parent), and 12.66 for the F1 offspring. We detected 202,349 high-quality SLAFs of which 144,972 were polymorphic; 10,042 SNPs were used to construct a genetic map that spanned 1,969.95 cM, with an average genetic distance of 0.23 cM between adjacent markers. This genetic map contains the largest molecular marker number of the grape maps so far reported. We thus demonstrate that SLAF-seq is a promising strategy for the construction of high-density genetic maps; the map that we report here is a good potential resource for QTL mapping of genes linked to major economic and agronomic traits, map-based cloning, and marker-assisted selection of grape.
Collapse
Affiliation(s)
- Jiahui Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
| | - Huiyang Xing
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning, P.R. China
- * E-mail: (YSG); (XWG)
| |
Collapse
|
31
|
Zeng B, Yan H, Liu X, Zang W, Zhang A, Zhou S, Huang L, Liu J. Genome-wide association study of rust traits in orchardgrass using SLAF-seq technology. Hereditas 2017; 154:5. [PMID: 28250720 PMCID: PMC5322626 DOI: 10.1186/s41065-017-0027-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 01/24/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND While orchardgrass (Dactylis glomerata L.) is a well-known perennial forage species, rust diseases cause serious reductions in the yield and quality of orchardgrass; however, genetic mechanisms of rust resistance are not well understood in orchardgrass. RESULTS In this study, a genome-wide association study (GWAS) was performed using specific-locus amplified fragment sequencing (SLAF-seq) technology in orchardgrass. A total of 2,334,889 SLAF tags were generated to produce 2,309,777 SNPs. ADMIXTURE analysis revealed unstructured subpopulations for 33 accessions, indicating that this orchardgrass population could be used for association analysis. Linkage disequilibrium (LD) analysis revealed an average r2 of 0.4 across all SNP pairs, indicating a high extent of LD in these samples. Through GWAS, a total of 4,604 SNPs were found to be significantly (P < 0.01) associated with the rust trait. The bulk analysis discovered a number of 5,211 SNPs related to rust trait. Two candidate genes, including cytochrome P450, and prolamin were implicated in disease resistance through prediction of functional genes surrounding each high-quality SNP (P < 0.01) associated with rust traits based on GWAS analysis and bulk analysis. CONCLUSIONS The large number of SNPs associated with rust traits and these two candidate genes may provide the basis for further research on rust resistance mechanisms and marker-assisted selection (MAS) for rust-resistant lineages.
Collapse
Affiliation(s)
- Bing Zeng
- Department of Animal Science, Southwest University, Rongchang, Chongqing, 402460 China
| | - Haidong Yan
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Xinchun Liu
- Agricultural College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Wenjing Zang
- College of Life Science, China West Normal University, Nanchong, 637009 China
| | - Ailing Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Sifan Zhou
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu, 611130 China
| | - Jinping Liu
- College of Life Science, China West Normal University, Nanchong, 637009 China
| |
Collapse
|
32
|
Su W, Wang L, Lei J, Chai S, Liu Y, Yang Y, Yang X, Jiao C. Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing. PLoS One 2017; 12:e0172066. [PMID: 28187178 PMCID: PMC5302839 DOI: 10.1371/journal.pone.0172066] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/30/2017] [Indexed: 01/18/2023] Open
Abstract
Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is cultivated worldwide. However, no genome-wide assessment of the genetic diversity of sweet potato has been reported to date. In the present study, the population structure and genetic diversity of 197 sweet potato accessions most of which were from China were assessed using 62,363 SNPs. A model-based structure analysis divided the accessions into three groups: group 1, group 2 and group 3. The genetic relationships among the accessions were evaluated using a phylogenetic tree, which clustered all the accessions into three major groups. A principal component analysis (PCA) showed that the accessions were distributed according to their population structure. The mean genetic distance among accessions ranged from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic information content (PIC) ranged from 0.232 for group 1 to 0.251 for group 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the maximum diversity was within accessions (89.569%). Using CoreHunter software, a core set of 39 accessions was obtained, which accounted for approximately 19.8% of the total collection. The core germplasm set of sweet potato developed will be a valuable resource for future sweet potato improvement strategies.
Collapse
Affiliation(s)
- Wenjin Su
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, China
| | - Lianjun Wang
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jian Lei
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Shasha Chai
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Yi Liu
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuanyuan Yang
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Xinsun Yang
- Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (XY); (CJ)
| | - Chunhai Jiao
- Hubei Academy of Agricultural Sciences, Wuhan, China
- * E-mail: (XY); (CJ)
| |
Collapse
|
33
|
Mei H, Liu Y, Du Z, Wu K, Cui C, Jiang X, Zhang H, Zheng Y. High-Density Genetic Map Construction and Gene Mapping of Basal Branching Habit and Flowers per Leaf Axil in Sesame. FRONTIERS IN PLANT SCIENCE 2017; 8:636. [PMID: 28496450 PMCID: PMC5406510 DOI: 10.3389/fpls.2017.00636] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 04/07/2017] [Indexed: 05/11/2023]
Abstract
A good genetic map can provide the framework for quantitative trait loci (QTL) analysis, map-based gene cloning, and genome sequence assembling. The main objectives of this study were to develop a high-density genetic linkage map using specific length amplified fragment sequencing (SLAF-seq) in sesame. In the result, a high-resolution genetic map with 9,378 SLAF markers and 13 linkage groups (LGs) was constructed. The map spanned a total genetic distance of 1,974.23 cM, and the mean LG length was 151.86 cM, with an average genetic distance of 0.22 cM between adjacent markers. Based on the newly constructed genetic map, genes for basal branching habit (SiBH) and flowers per leaf axil (SiFA) were mapped to LG5 and LG11, respectively.
Collapse
|
34
|
Xie D, Dai Z, Yang Z, Sun J, Zhao D, Yang X, Zhang L, Tang Q, Su J. Genome-Wide Association Study Identifying Candidate Genes Influencing Important Agronomic Traits of Flax ( Linum usitatissimum L.) Using SLAF-seq. FRONTIERS IN PLANT SCIENCE 2017; 8:2232. [PMID: 29375606 PMCID: PMC5767239 DOI: 10.3389/fpls.2017.02232] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2017] [Accepted: 12/19/2017] [Indexed: 05/13/2023]
Abstract
Flax (Linum usitatissimum L.) is an important cash crop, and its agronomic traits directly affect yield and quality. Molecular studies on flax remain inadequate because relatively few flax genes have been associated with agronomic traits or have been identified as having potential applications. To identify markers and candidate genes that can potentially be used for genetic improvement of crucial agronomic traits, we examined 224 specimens of core flax germplasm; specifically, phenotypic data for key traits, including plant height, technical length, number of branches, number of fruits, and 1000-grain weight were investigated under three environmental conditions before specific-locus amplified fragment sequencing (SLAF-seq) was employed to perform a genome-wide association study (GWAS) for these five agronomic traits. Subsequently, the results were used to screen single nucleotide polymorphism (SNP) loci and candidate genes that exhibited a significant correlation with the important agronomic traits. Our analyses identified a total of 42 SNP loci that showed significant correlations with the five important agronomic flax traits. Next, candidate genes were screened in the 10 kb zone of each of the 42 SNP loci. These SNP loci were then analyzed by a more stringent screening via co-identification using both a general linear model (GLM) and a mixed linear model (MLM) as well as co-occurrences in at least two of the three environments, whereby 15 final candidate genes were obtained. Based on these results, we determined that UGT and PL are candidate genes for plant height, GRAS and XTH are candidate genes for the number of branches, Contig1437 and LU0019C12 are candidate genes for the number of fruits, and PHO1 is a candidate gene for the 1000-seed weight. We propose that the identified SNP loci and corresponding candidate genes might serve as a biological basis for improving crucial agronomic flax traits.
Collapse
Affiliation(s)
- Dongwei Xie
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Zhigang Dai
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Zemao Yang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jian Sun
- College of Agriculture, Northeast Agricultural University, Harbin, China
| | - Debao Zhao
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Xue Yang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Liguo Zhang
- Institute of Industrial Crops, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Qing Tang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jianguang Su
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
- *Correspondence: Jianguang Su
| |
Collapse
|
35
|
Bai ZY, Han XK, Liu XJ, Li QQ, Li JL. Construction of a high-density genetic map and QTL mapping for pearl quality-related traits in Hyriopsis cumingii. Sci Rep 2016; 6:32608. [PMID: 27587236 PMCID: PMC5009340 DOI: 10.1038/srep32608] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/11/2016] [Indexed: 11/22/2022] Open
Abstract
A high-density genetic map is essential for quantitative trait locus (QTL) fine mapping. In this study, 4,508 effective single nucleotide polymorphism markers (detected using specific-locus amplified fragment sequencing) and 475 microsatellites were mapped to 19 linkage groups (LGs) using a family with 157 individuals. The map spanned 2,713 cM, with an average of 259 markers and 79 loci per LG and an average inter-marker distance of 1.81 cM. To identify QTLs for pearl quality traits, 26 putatively significant QTLs were detected for 10 traits, including, three for shell width, seven for body weight, two for shell weight, two for margin mantle weight, five for inner mantle weight, and seven for shell nacre colour. Among them, five QTLs associated with shell nacre colour were mapped to LG17 and explained 19.7% to 22.8% of the trait variation; this suggests that some important genes or loci determine shell nacre colour in LG17. The linkage map and mapped QTLs for shell nacre colour would be useful for improving the quality of Hyriopsis cumingii via marker-assisted selection.
Collapse
Affiliation(s)
- Zhi-Yi Bai
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
| | - Xue-Kai Han
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Xiao-Jun Liu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Qing-Qing Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
| | - Jia-Le Li
- Key Laboratory of Freshwater Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Agriculture, Shanghai 201306, China
- Shanghai Engineering Research Centre of Aquaculture, Shanghai Ocean University, Shanghai 201306, China
- Aquaculture Division, E-Institute of Shanghai Universities, Shanghai Ocean University, Shanghai 201306, China
| |
Collapse
|
36
|
Ye Y, Cai M, Ju Y, Jiao Y, Feng L, Pan H, Cheng T, Zhang Q. Identification and Validation of SNP Markers Linked to Dwarf Traits Using SLAF-Seq Technology in Lagerstroemia. PLoS One 2016; 11:e0158970. [PMID: 27404662 PMCID: PMC4942086 DOI: 10.1371/journal.pone.0158970] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 06/26/2016] [Indexed: 11/18/2022] Open
Abstract
The genetic control of plant architecture is a promising approach to breed desirable cultivars, particularly in ornamental flowers. In this study, the F1 population (142 seedlings) derived from Lagerstroemia fauriei (non-dwarf) × L. indica 'Pocomoke' (dwarf) was phenotyped for six traits (plant height (PH), internode length (IL), internode number, primary lateral branch height (PLBH), secondary lateral branch height and primary branch number), and the IL and PLBH traits were positively correlated with the PH trait and considered representative indexes of PH. Fifty non-dwarf and dwarf seedlings were pooled and subjected to a specific-locus amplified fragment sequencing (SLAF-seq) method, which screened 1221 polymorphic markers. A total of 3 markers segregating between bulks were validated in the F1 population, with the M16337 and M38412 markers highly correlated with the IL trait and the M25207 marker highly correlated with the PLBH trait. These markers provide a predictability of approximately 80% using a single marker (M25207) and a predictability of 90% using marker combinations (M16337 + M25207) in the F1 population, which revealed that the IL and the PLBH traits, especially the PLBH, were the decisive elements for PH in terms of molecular regulation. Further validation was performed in the BC1 population and a set of 28 Lagerstroemia stocks using allele-specific PCR (AS-PCR) technology, and the results showed the stability and reliability of the SNP markers and the co-determination of PH by multiple genes. Our findings provide an important theoretical and practical basis for the early prediction and indirect selection of PH using the IL and the PLBH, and the detected SNPs may be useful for marker-assisted selection (MAS) in crape myrtle.
Collapse
Affiliation(s)
- Yuanjun Ye
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Ming Cai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yiqian Ju
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Yao Jiao
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Lu Feng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| |
Collapse
|
37
|
Zhao X, Huang L, Zhang X, Wang J, Yan D, Li J, Tang L, Li X, Shi T. Construction of high-density genetic linkage map and identification of flowering-time QTLs in orchardgrass using SSRs and SLAF-seq. Sci Rep 2016; 6:29345. [PMID: 27389619 PMCID: PMC4937404 DOI: 10.1038/srep29345] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 06/17/2016] [Indexed: 11/09/2022] Open
Abstract
Orchardgrass (Dactylis glomerata L.) is one of the most economically important perennial, cool-season forage species grown and pastured worldwide. High-density genetic linkage mapping is a valuable and effective method for exploring complex quantitative traits. In this study, we developed 447,177 markers based on SLAF-seq and used them to perform a comparative genomics analysis. Perennial ryegrass sequences were the most similar (5.02%) to orchardgrass sequences. A high-density linkage map of orchardgrass was constructed using 2,467 SLAF markers and 43 SSRs, which were distributed on seven linkage groups spanning 715.77 cM. The average distance between adjacent markers was 0.37 cM. Based on phenotyping in four environments, 11 potentially significant quantitative trait loci (QTLs) for two target traits–heading date (HD) and flowering time (FT)–were identified and positioned on linkage groups LG1, LG3, and LG5. Significant QTLs explained 8.20–27.00% of the total phenotypic variation, with the LOD ranging from 3.85–12.21. Marker167780 and Marker139469 were associated with FT and HD at the same location (Ya’an) over two different years. The utility of SLAF markers for rapid generation of genetic maps and QTL analysis has been demonstrated for heading date and flowering time in a global forage grass.
Collapse
Affiliation(s)
- Xinxin Zhao
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linkai Huang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinquan Zhang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jianping Wang
- Agronomy Department, University of Florida, FL, 32610, USA
| | - Defei Yan
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ji Li
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Lu Tang
- Department of Grassland Science, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiaolong Li
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Tongwei Shi
- Biomarker Technologies Corporation, Beijing, 101300, China
| |
Collapse
|
38
|
Zhang J, Yuan H, Li M, Li Y, Wang Y, Ma X, Zhang Y, Tan F, Wu R. A High-Density Genetic Map of Tetraploid Salix matsudana Using Specific Length Amplified Fragment Sequencing (SLAF-seq). PLoS One 2016; 11:e0157777. [PMID: 27327501 PMCID: PMC4915623 DOI: 10.1371/journal.pone.0157777] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/03/2016] [Indexed: 01/20/2023] Open
Abstract
As a salt-tolerant arbor tree species, Salix matsudana plays an important role in afforestation and greening in the coastal areas of China. To select superior Salix varieties that adapt to wide saline areas, it is of paramount importance to understand and identify the mechanisms of salt-tolerance at the level of the whole genome. Here, we describe a high-density genetic linkage map of S. matsudana that represents a good coverage of the Salix genome. An intraspecific F1 hybrid population was established by crossing the salt-sensitive “Yanjiang” variety as the female parent with the salt-tolerant “9901” variety as the male parent. This population, along with its parents, was genotyped by specific length amplified fragment sequencing (SLAF-seq), leading to 277,333 high-quality SLAF markers. By marker analysis, we found that both the parents and offspring were tetraploid. The mean sequencing depth was 53.20-fold for “Yanjiang”, 47.41-fold for “9901”, and 11.02-fold for the offspring. Of the SLAF markers detected, 42,321 are polymorphic with sufficient quality for map construction. The final genetic map was constructed using 6,737 SLAF markers, covering 38 linkage groups (LGs). The genetic map spanned 5,497.45 cM in length, with an average distance of 0.82 cM. As a first high-density genetic map of S. matsudana constructed from salt tolerance-varying varieties, this study will provide a foundation for mapping quantitative trait loci that modulate salt tolerance and resistance in Salix and provide important references for molecular breeding of this important forest tree.
Collapse
Affiliation(s)
- Jian Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Huwei Yuan
- National Engineering Laboratory for Forest Tree Breeding, Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants of Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Min Li
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Yujuan Li
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Ying Wang
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Xiangjian Ma
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Yuan Zhang
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Feng Tan
- Jiangsu Riverine Institute of Agricultural Sciences, Rugao, Jiangsu, China
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Center for Statistical Genetics, Pennsylvania State University, Hershey, United States of America
- * E-mail: ;
| |
Collapse
|
39
|
Zhang Z, Shang H, Shi Y, Huang L, Li J, Ge Q, Gong J, Liu A, Chen T, Wang D, Wang Y, Palanga KK, Muhammad J, Li W, Lu Q, Deng X, Tan Y, Song W, Cai J, Li P, Rashid HO, Gong W, Yuan Y. Construction of a high-density genetic map by specific locus amplified fragment sequencing (SLAF-seq) and its application to Quantitative Trait Loci (QTL) analysis for boll weight in upland cotton (Gossypium hirsutum.). BMC PLANT BIOLOGY 2016; 16:79. [PMID: 27067834 PMCID: PMC4827241 DOI: 10.1186/s12870-016-0741-4] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 02/17/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND Upland Cotton (Gossypium hirsutum) is one of the most important worldwide crops it provides natural high-quality fiber for the industrial production and everyday use. Next-generation sequencing is a powerful method to identify single nucleotide polymorphism markers on a large scale for the construction of a high-density genetic map for quantitative trait loci mapping. RESULTS In this research, a recombinant inbred lines population developed from two upland cotton cultivars 0-153 and sGK9708 was used to construct a high-density genetic map through the specific locus amplified fragment sequencing method. The high-density genetic map harbored 5521 single nucleotide polymorphism markers which covered a total distance of 3259.37 cM with an average marker interval of 0.78 cM without gaps larger than 10 cM. In total 18 quantitative trait loci of boll weight were identified as stable quantitative trait loci and were detected in at least three out of 11 environments and explained 4.15-16.70 % of the observed phenotypic variation. In total, 344 candidate genes were identified within the confidence intervals of these stable quantitative trait loci based on the cotton genome sequence. These genes were categorized based on their function through gene ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and eukaryotic orthologous groups analysis. CONCLUSIONS This research reported the first high-density genetic map for Upland Cotton (Gossypium hirsutum) with a recombinant inbred line population using single nucleotide polymorphism markers developed by specific locus amplified fragment sequencing. We also identified quantitative trait loci of boll weight across 11 environments and identified candidate genes within the quantitative trait loci confidence intervals. The results of this research would provide useful information for the next-step work including fine mapping, gene functional analysis, pyramiding breeding of functional genes as well as marker-assisted selection.
Collapse
Affiliation(s)
- Zhen Zhang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Haihong Shang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yuzhen Shi
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Long Huang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Junwen Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Qun Ge
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Juwu Gong
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Aiying Liu
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Tingting Chen
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Dan Wang
- />Biomarker Technologies Corporation, Beijing, 103100 China
| | - Yanling Wang
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Koffi Kibalou Palanga
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Jamshed Muhammad
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Weijie Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Quanwei Lu
- />Anyang Institute of Technology, Anyang, 455000 Henan China
| | - Xiaoying Deng
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yunna Tan
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Weiwu Song
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Juan Cai
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Pengtao Li
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Harun or Rashid
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wankui Gong
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Youlu Yuan
- />State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| |
Collapse
|
40
|
Zhao Z, Gu H, Sheng X, Yu H, Wang J, Huang L, Wang D. Genome-Wide Single-Nucleotide Polymorphisms Discovery and High-Density Genetic Map Construction in Cauliflower Using Specific-Locus Amplified Fragment Sequencing. FRONTIERS IN PLANT SCIENCE 2016; 7:334. [PMID: 27047515 PMCID: PMC4800193 DOI: 10.3389/fpls.2016.00334] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 03/04/2016] [Indexed: 05/19/2023]
Abstract
Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1776 high-quality SLAF markers, including 2741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower.
Collapse
Affiliation(s)
- Zhenqing Zhao
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Honghui Gu
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Xiaoguang Sheng
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Huifang Yu
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Jiansheng Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural SciencesHangzhou, China
| | - Long Huang
- Biomarker Technologies CorporationBeijing, China
| | - Dan Wang
- Biomarker Technologies CorporationBeijing, China
| |
Collapse
|
41
|
Xu X, Chao J, Cheng X, Wang R, Sun B, Wang H, Luo S, Xu X, Wu T, Li Y. Mapping of a Novel Race Specific Resistance Gene to Phytophthora Root Rot of Pepper (Capsicum annuum) Using Bulked Segregant Analysis Combined with Specific Length Amplified Fragment Sequencing Strategy. PLoS One 2016; 11:e0151401. [PMID: 26992080 PMCID: PMC4798474 DOI: 10.1371/journal.pone.0151401] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 02/26/2016] [Indexed: 11/19/2022] Open
Abstract
Phytophthora root rot caused by Phytophthora capsici (P. capsici) is a serious limitation to pepper production in Southern China, with high temperature and humidity. Mapping PRR resistance genes can provide linked DNA markers for breeding PRR resistant varieties by molecular marker-assisted selection (MAS). Two BC1 populations and an F2 population derived from a cross between P. capsici-resistant accession, Criollo de Morelos 334 (CM334) and P. capsici-susceptible accession, New Mexico Capsicum Accession 10399 (NMCA10399) were used to investigate the genetic characteristics of PRR resistance. PRR resistance to isolate Byl4 (race 3) was controlled by a single dominant gene, PhR10, that was mapped to an interval of 16.39Mb at the end of the long arm of chromosome 10. Integration of bulked segregant analysis (BSA) and Specific Length Amplified Fragment sequencing (SLAF-seq) provided an efficient genetic mapping strategy. Ten polymorphic Simple Sequence Repeat (SSR) markers were found within this region and used to screen the genotypes of 636 BC1 plants, delimiting PhR10 to a 2.57 Mb interval between markers P52-11-21 (1.5 cM away) and P52-11-41 (1.1 cM). A total of 163 genes were annotated within this region and 31 were predicted to be associated with disease resistance. PhR10 is a novel race specific gene for PRR, and this paper describes linked SSR markers suitable for marker-assisted selection of PRR resistant varieties, also laying a foundation for cloning the resistance gene.
Collapse
Affiliation(s)
- Xiaomei Xu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Lab for New Technology Research of Vegetables, Guangzhou, China
| | - Juan Chao
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Lab for New Technology Research of Vegetables, Guangzhou, China
| | - Xueli Cheng
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Lab for New Technology Research of Vegetables, Guangzhou, China
| | - Rui Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Lab for New Technology Research of Vegetables, Guangzhou, China
| | - Baojuan Sun
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Lab for New Technology Research of Vegetables, Guangzhou, China
| | - Hengming Wang
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Shaobo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Lab for New Technology Research of Vegetables, Guangzhou, China
| | - Xiaowan Xu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Tingquan Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Key Lab for New Technology Research of Vegetables, Guangzhou, China
| | - Ying Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| |
Collapse
|
42
|
Zhang D, Li H, Wang J, Zhang H, Hu Z, Chu S, Lv H, Yu D. High-Density Genetic Mapping Identifies New Major Loci for Tolerance to Low-Phosphorus Stress in Soybean. FRONTIERS IN PLANT SCIENCE 2016; 7:372. [PMID: 27065041 PMCID: PMC4811872 DOI: 10.3389/fpls.2016.00372] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 03/11/2016] [Indexed: 05/18/2023]
Abstract
Phosphorus (P) is essential for all living cells and organisms, and low-P stress represents a major constraint on plant growth and yield worldwide. Soybean is an important economical resource of protein and oil for human and animals, and soybean is also a high-P demand species that is sensitive to low-P stress, which is considered a major constraint on soybean production. However, P efficiency is an important complex quantitative trait involving multiple genes, and the mechanisms underlying soybean P efficiency are largely unknown. Here, we reported the construction of a high-density genetic map using a specific-locus amplified fragment sequencing (SLAF-seq) strategy in soybean. This map, spanning 3020.59 cM in length, contained 6159 markers on 20 chromosomes, with an average distance of 0.49 cM between adjacent markers. Based on this map, 20 loci, including eight novel loci, associated with P efficiency-related traits were identified across multiple years and treatments. The confidence intervals of almost all QTLs were refined significantly, and the accuracy of this map was evidenced by coincident detections of the previously identified P efficiency-related genes GmACP1 and GmPT1. Notably, a highly significant novel QTL located on chromosome 4, q4-2, was identified across traits, years and treatments. Several candidate genes, such as a pectin methylesterase-encoding gene (Glyma.04G214000) and a protein kinase gene (Glyma.13G161900), with significantly differential expression upon low-P stress were considered as promising candidates involved in regulating soybean P efficiency. Markers that tightly associated with P efficiency could be used for marker-assisted selection in a soybean P efficient breeding program. Further, dissection of these QTLs will facilitate gene cloning underlying P efficiency in soybean, and increase our understanding of efficient use of P in enhancing crop yield.
Collapse
Affiliation(s)
- Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural UniversityZhengzhou, China
- *Correspondence: Dan Zhang
| | - Hongyan Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural UniversityZhengzhou, China
| | - Jinshe Wang
- Zhengzhou National Subcenter for Soybean Improvement/Key Laboratory of Oil Crops in Huanghuaihai Plains, Institute of Industrial Crops, Henan Academy of Agricultural SciencesZhengzhou, China
| | - Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
| | - Zhenbin Hu
- Agronomy Department, Kansas State UniversityManhattan, KS, USA
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural UniversityZhengzhou, China
| | - Haiyan Lv
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural UniversityZhengzhou, China
| | - Deyue Yu
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Nanjing Agricultural UniversityNanjing, China
| |
Collapse
|
43
|
Hu MJ, Zhang HP, Liu K, Cao JJ, Wang SX, Jiang H, Wu ZY, Lu J, Zhu XF, Xia XC, Sun GL, Ma CX, Chang C. Cloning and Characterization of TaTGW-7A Gene Associated with Grain Weight in Wheat via SLAF-seq-BSA. FRONTIERS IN PLANT SCIENCE 2016; 7:1902. [PMID: 28066462 PMCID: PMC5167734 DOI: 10.3389/fpls.2016.01902] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 12/01/2016] [Indexed: 05/18/2023]
Abstract
Thousand-grain weight (TGW) of wheat (Triticum aestivum L.) contributes significantly to grain yield. In the present study, a candidate gene associated with TGW was identified through specific-locus amplified fragment sequencing (SLAF-seq) of DNA bulks of recombinant inbred lines (RIL) derived from the cross between Jing 411 and Hongmangchun 21. The gene was located on chromosome 7A, designated as TaTGW-7A with a complete genome sequence and an open reading frame (ORF). A single nucleotide polymorphism (SNP) was present in the first exon between two alleles at TaTGW-7A locus, resulting in a Val to Ala substitution, corresponding to a change from higher to lower TGW. Cleaved amplified polymorphic sequence (CAPS) (TGW7A) and InDel (TG9) markers were developed to discriminate the two alleles TaTGW-7Aa and TaTGW-7Ab for higher and lower TGW, respectively. A major QTL co-segregating with TaTGW-7A explained 21.7-27.1% of phenotypic variance for TGW in the RIL population across five environments. The association of TaTGW-7A with TGW was further validated in a natural population and Chinese mini-core collections. Quantitative real-time PCR revealed higher transcript levels of TaTGW-7Aa than those of TaTGW-7Ab during grain development. High frequencies of the superior allele TaTGW-7Aa for higher TGW in Chinese mini-core collections (65.0%) and 501 wheat varieties (86.0%) indicated a strong and positive selection of this allele in wheat breeding. The molecular markers TGW7A and TG9 can be used for improvement of TGW in breeding programs.
Collapse
Affiliation(s)
- Ming-Jian Hu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Hai-Ping Zhang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Kai Liu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Jia-Jia Cao
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Sheng-Xing Wang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Hao Jiang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Zeng-Yun Wu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Xiao F. Zhu
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Xian-Chun Xia
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- National Wheat Improvement Center/The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Gen-Lou Sun
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- Department of Biology, Saint Mary’s University, HalifaxNS, Canada
| | - Chuan-Xi Ma
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
| | - Cheng Chang
- College of Agronomy, Anhui Agricultural University – Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, The Ministry of AgricultureHefei, China
- *Correspondence: Cheng Chang,
| |
Collapse
|
44
|
Luo C, Shu B, Yao Q, Wu H, Xu W, Wang S. Construction of a High-Density Genetic Map Based on Large-Scale Marker Development in Mango Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). FRONTIERS IN PLANT SCIENCE 2016; 7:1310. [PMID: 27625670 PMCID: PMC5003885 DOI: 10.3389/fpls.2016.01310] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 08/16/2016] [Indexed: 05/22/2023]
Abstract
Genetic maps are particularly important and valuable tools for quantitative trait locus (QTL) mapping and marker assisted selection (MAS) of plant with desirable traits. In this study, 173 F1 plants from a cross between Mangifera indica L. "Jin-Hwang" and M. indica L. "Irwin" and their parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 66.02 Gb of raw data containing 330.64 M reads were obtained. A total of 318,414 SLAFs were detected, of which 156,368 were polymorphic. Finally, 6594 SLAFs were organized into a linkage map consisting of 20 linkage groups (LGs). The total length of the map was 3148.28 cM and the average distance between adjacent markers was 0.48 cM. This map could be considered, to our knowledge, the first high-density genetic map of mango, and might form the basis for fine QTL mapping and MAS of mango.
Collapse
|
45
|
Zhu WY, Huang L, Chen L, Yang JT, Wu JN, Qu ML, Yao DQ, Guo CL, Lian HL, He HL, Pan JS, Cai R. A High-Density Genetic Linkage Map for Cucumber (Cucumis sativus L.): Based on Specific Length Amplified Fragment (SLAF) Sequencing and QTL Analysis of Fruit Traits in Cucumber. FRONTIERS IN PLANT SCIENCE 2016; 7:437. [PMID: 27148281 PMCID: PMC4835494 DOI: 10.3389/fpls.2016.00437] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 03/21/2016] [Indexed: 05/10/2023]
Abstract
High-density genetic linkage map plays an important role in genome assembly and quantitative trait loci (QTL) fine mapping. Since the coming of next-generation sequencing, makes the structure of high-density linkage maps much more convenient and practical, which simplifies SNP discovery and high-throughput genotyping. In this research, a high-density linkage map of cucumber was structured using specific length amplified fragment sequencing, using 153 F2 populations of S1000 × S1002. The high-density genetic map composed 3,057 SLAFs, including 4,475 SNP markers on seven chromosomes, and spanned 1061.19 cM. The average genetic distance is 0.35 cM. Based on this high-density genome map, QTL analysis was performed on two cucumber fruit traits, fruit length and fruit diameter. There are 15 QTLs for the two fruit traits were detected.
Collapse
Affiliation(s)
- Wen-Ying Zhu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Long Huang
- Biomarker Technologies CorporationBeijing, China
| | - Long Chen
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jian-Tao Yang
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jia-Ni Wu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Mei-Ling Qu
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | | | - Chun-Li Guo
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Hong-Li Lian
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Huan-Le He
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
| | - Jun-Song Pan
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
- *Correspondence: Jun-Song Pan, ; Run Cai,
| | - Run Cai
- School of Agriculture and Biology, Shanghai Jiaotong UniversityShanghai, China
- *Correspondence: Jun-Song Pan, ; Run Cai,
| |
Collapse
|
46
|
Pawełkowicz M, Zieliński K, Zielińska D, Pląder W, Yagi K, Wojcieszek M, Siedlecka E, Bartoszewski G, Skarzyńska A, Przybecki Z. Next generation sequencing and omics in cucumber (Cucumis sativus L.) breeding directed research. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 242:77-88. [PMID: 26566826 DOI: 10.1016/j.plantsci.2015.07.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 06/29/2015] [Accepted: 07/28/2015] [Indexed: 05/10/2023]
Abstract
In the post-genomic era the availability of genomic tools and resources is leading us to novel generation methods in plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. In this study we have mainly concentrated on the Cucumis sativus and (but much less) Cucurbitaceae family several important vegetable crops. There are many reports on research conducted in Cucurbitaceae plant breeding programs on the ripening process, phloem transport, disease resistance, cold tolerance and fruit quality traits. This paper presents the role played by new omic technologies in the creation of knowledge on the mechanisms of the formation of the breeding features. The analysis of NGS (NGS-next generation sequencing) data allows the discovery of new genes and regulatory sequences, their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Firstly a high density map should be created for the reference genome, then each re-sequencing data could be mapped and new markers brought out into breeding populations. The paper also presents methods that could be used in the future for the creation of variability and genomic modification of the species in question. It has been shown also the state and usefulness in breeding the chloroplastomic and mitochondriomic study.
Collapse
Affiliation(s)
- Magdalena Pawełkowicz
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Konrad Zieliński
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Dorota Zielińska
- Department of Food Gastronomy and Food Hygiene, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Wojciech Pląder
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Kouhei Yagi
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Michał Wojcieszek
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Ewa Siedlecka
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Grzegorz Bartoszewski
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Agnieszka Skarzyńska
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland
| | - Zbigniew Przybecki
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland.
| |
Collapse
|
47
|
Jiang B, Liu W, Xie D, Peng Q, He X, Lin Y, Liang Z. High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:1035. [PMID: 26647294 PMCID: PMC4673774 DOI: 10.1186/s12864-015-2220-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/16/2015] [Indexed: 11/10/2022] Open
Abstract
Background High-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Specific-locus amplified fragment sequencing (SLAF-seq) is a newly developed high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping. Results In our present study, we constructed a high-density genetic map by using SLAF-seq and identified a locus controlling pericarp color in wax gourd. An F2 population of 140 individuals and their two parents were subjected to SLAF-seq. A total of 143.38 M pair-end reads were generated. The average sequencing depth was 26.51 in the maternal line (B214), 27.01 in the parental line (B227), and 5.11 in each F2 individual. When filtering low-depth SLAF tags, a total of 142,653 high-quality SLAFs were detected, and 22,151 of them were polymorphic, with a polymorphism rate of 15.42 %. And finally, 4,607 of the polymorphic markers were selected for genetic map construction, and 12 linkage groups (LGs) were generated. The map spanned 2,172.86 cM with an average distance between adjacent markers for 0.49 cM. The inheritance of pericarp color was also studied, which showed that the pericarp color was controlled by one single gene. And based on the newly constructed high-density map, a single locus locating on chromosome 5 was identified for controlling the pericarp color of wax gourd. Conclusions This is the first report of high-density genetic map construction and gene mapping in wax gourd, which will be served as an invaluable tool for gene mapping, marker assisted breeding, map-based gene cloning, comparative mapping and draft genome assembling of wax gourd. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2220-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China. .,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China.
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Yu'e Lin
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Zhaojun Liang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| |
Collapse
|
48
|
Wen C, Mao A, Dong C, Liu H, Yu S, Guo YD, Weng Y, Xu Y. Fine genetic mapping of target leaf spot resistance gene cca-3 in cucumber, Cucumis sativus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2495-506. [PMID: 26385372 DOI: 10.1007/s00122-015-2604-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/29/2015] [Indexed: 05/26/2023]
Abstract
The cucumber target leaf spot resistance gene cca - 3 was fine mapped in a 79-kb region harboring a CC-NB-ARC type R gene that may be responsible for the hypersensitive responses to infection of the target leaf spot pathogen in cucumber. The target leaf spot (TLS) is one of the most important foliar diseases in cucumber (Cucumis sativus L.). In this study, we conducted fine genetic mapping of a simply inherited recessive resistance gene, cca-3 against TLS with 193 F2:3 families and 890 F2 plants derived from the resistant cucumber inbred line D31 and the susceptible line D5. Initial mapping with microsatellite markers and bulked segregant analysis placed cca-3 in a 2.5-Mbp region of cucumber chromosome 6. The D5 and D31 lines were re-sequenced at 10× genome coverage to explore new markers in the target region. Genetic mapping in the large F2 population delimited the cca-3 locus in a 79-kb region with flanking markers Indel16874230 and Indel16953846. Additional fine mapping and gene annotation in this region revealed that a CC-NB-ARC type resistance gene analog, Csa6M375730, seems to be the candidate gene for cca-3. One single nucleotide polymorphism (SNP) was found in the NB-ARC domain of this candidate gene sequence between D31 and D5 that may lead to amino acid change, thus altering the function of the conserved NB-ARC motif. This SNP was validated in the segregating population as well as 24 independent cucumber lines. There was significantly higher level of cca-3 expression in the leaves of D5 (susceptible) than in D31 (resistant), and the expression level was positively correlated with the areas of necrotic spots on leaves after inoculation. It seems the cca-3 resistance gene was able to induce hypersensitive responses to the infection by TLS pathogen.
Collapse
Affiliation(s)
- Changlong Wen
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| | - Aijun Mao
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Congjuan Dong
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Huyu Liu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Shuancang Yu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Yang-Dong Guo
- College of Agriculture and Biotechnology, China Agricultural University, Beijing, 100193, China.
| | - Yiqun Weng
- USDA-ARS, Vegetable Crops Research Unit, Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| |
Collapse
|
49
|
Shan T, Pang S, Li J, Li X, Su L. Construction of a high-density genetic map and mapping of a sex-linked locus for the brown alga Undaria pinnatifida (Phaeophyceae) based on large scale marker development by specific length amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:902. [PMID: 26541547 PMCID: PMC4635539 DOI: 10.1186/s12864-015-2184-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 11/03/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida. RESULTS A total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region. CONCLUSIONS A high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.
Collapse
Affiliation(s)
- Tifeng Shan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Shaojun Pang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
| | - Jing Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Xia Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| | - Li Su
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, PR China.
- Graduate University of Chinese Academy of Science, Beijing, 100049, PR China.
| |
Collapse
|
50
|
Xu X, Lu L, Zhu B, Xu Q, Qi X, Chen X. QTL mapping of cucumber fruit flesh thickness by SLAF-seq. Sci Rep 2015; 5:15829. [PMID: 26508560 PMCID: PMC4623748 DOI: 10.1038/srep15829] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/21/2015] [Indexed: 11/24/2022] Open
Abstract
Cucumber is an agriculturally and economically important vegetable crop worldwide. Fruit flesh thickness is an important trait for cucumber and also a central determinant of yield, yet little is known about the underlying mechanism of this trait. In this study, bulked segregant analysis (BSA) combined with specific length amplified fragment sequencing (SLAF-seq) was applied to finely map the gene that underlies fruit flesh thickness in cucumber. A 0.19-Mb-long quantitative trait locus on chromosome 2 controlling fruit flesh thickness (QTL fft2.1) was identified and further confirmed by simple sequence repeat (SSR) marker-based classical QTL mapping in 138 F2 individuals. Gene prediction of this 0.19-Mb region identified 20 genes. Quantitative RT-PCR revealed higher expression levels of Csa2 M058670.1 (SET domain protein-lysine methyltransferase) in D8 (thick fruit flesh parent) compared with that in XUE1 (thin fruit flesh parent) during fruit development. Sequence alignment analysis of Csa2M058670.1 from thick and thin fruit flesh cucumber lines revealed a 4-bp deletion mutation in the promoter region of this candidate gene, which may result in the loss of Csa2M058670.1 activation in thin fruit flesh lines. The data presented herein suggest that Csa2M058670.1 is a possible candidate gene for controlling flesh thickness in cucumber.
Collapse
Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Lu Lu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Biyun Zhu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou, Jiangsu 225009, China
| |
Collapse
|