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de Jong TV, Pan Y, Rastas P, Munro D, Tutaj M, Akil H, Benner C, Chen D, Chitre AS, Chow W, Colonna V, Dalgard CL, Demos WM, Doris PA, Garrison E, Geurts AM, Gunturkun HM, Guryev V, Hourlier T, Howe K, Huang J, Kalbfleisch T, Kim P, Li L, Mahaffey S, Martin FJ, Mohammadi P, Ozel AB, Polesskaya O, Pravenec M, Prins P, Sebat J, Smith JR, Solberg Woods LC, Tabakoff B, Tracey A, Uliano-Silva M, Villani F, Wang H, Sharp BM, Telese F, Jiang Z, Saba L, Wang X, Murphy TD, Palmer AA, Kwitek AE, Dwinell MR, Williams RW, Li JZ, Chen H. A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats. Cell Genom 2024; 4:100527. [PMID: 38537634 PMCID: PMC11019364 DOI: 10.1016/j.xgen.2024.100527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/26/2023] [Accepted: 02/29/2024] [Indexed: 04/09/2024]
Abstract
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared with its predecessor. Gene annotations are now more complete, improving the mapping precision of genomic, transcriptomic, and proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ∼20.0 million sequence variations, of which 18,700 are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
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Affiliation(s)
- Tristan V de Jong
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Yanchao Pan
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Daniel Munro
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Department of Integrative Structural and Computational Biology, Scripps Research, San Diego, CA, USA
| | - Monika Tutaj
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Huda Akil
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI, USA
| | - Chris Benner
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Denghui Chen
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Apurva S Chitre
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - William Chow
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Vincenza Colonna
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy; Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Wendy M Demos
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Peter A Doris
- The Brown Foundation Institute of Molecular Medicine, Center for Human Genetics, University of Texas Health Science Center, Houston, TX, USA
| | - Erik Garrison
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Aron M Geurts
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Hakan M Gunturkun
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Victor Guryev
- Genome Structure and Ageing, University of Groningen, UMC, Groningen, the Netherlands
| | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Kerstin Howe
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | - Jun Huang
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ted Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Louisville, KY, USA
| | - Panjun Kim
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Ling Li
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Spencer Mahaffey
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus in Hinxton, Cambridgeshire, UK
| | - Pejman Mohammadi
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Oksana Polesskaya
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Michal Pravenec
- Institute of Physiology, Czech Academy of Sciences, Prague, Czechia
| | - Pjotr Prins
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jonathan Sebat
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Jennifer R Smith
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Leah C Solberg Woods
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Boris Tabakoff
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Alan Tracey
- Tree of Life, Wellcome Sanger Institute, Cambridge, UK
| | | | - Flavia Villani
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Hongyang Wang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Burt M Sharp
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Francesca Telese
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA
| | - Zhihua Jiang
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
| | - Laura Saba
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Xusheng Wang
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Terence D Murphy
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, San Diego, CA, USA; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Anne E Kwitek
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Melinda R Dwinell
- Department of Physiology, Medical College of Wisconsin, Milwaukee, WI, USA; Rat Genome Database, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Robert W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
| | - Hao Chen
- Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
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Zhang L, Luo Y, Zhong X, Jia G, Chen H, Wang Y, Zhou J, Ma C, Li X, Huang K, Yang S, Wang J, Han D, Ren Y, Cai L, Zhou X. Genome-wide QTL mapping for agronomic traits in the winter wheat cultivar Pindong 34 based on 90K SNP array. Front Plant Sci 2024; 15:1369440. [PMID: 38638350 PMCID: PMC11024375 DOI: 10.3389/fpls.2024.1369440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Accepted: 03/11/2024] [Indexed: 04/20/2024]
Abstract
Introduction Agronomic traits are key components of wheat yield. Exploitation of the major underlying quantitative trait loci (QTLs) can improve the yield potential in wheat breeding. Methods In this study, we constructed a recombinant inbred line (RIL) population from Mingxian 169 (MX169) and Pindong 34 (PD34) to determine the QTLs for grain length (GL), grain width (GW), grain length-to-width ratio (LWR), plant height (PH), spike length (SL), grain number per spike (GNS), and the thousand grain weight (TGW) across four environments using wheat 90K SNP array. Results A QTL associated with TGW, i.e., QTGWpd.swust-6BS, was identified on chromosome 6B, which explained approximately 14.1%-16.2% of the phenotypic variation. In addition, eight QTLs associated with GL were detected across six chromosomes in four different test environments. These were QGLpd.swust-1BL, QGLpd.swust-2BL, QGLpd.swust-3BL.1, QGLpd.swust-3BL.2, QGLpd.swust-5DL, QGLpd.swust-6AL, QGLpd.swust-6DL.1, and QGLpd.swust-6DL.2. They accounted for 9.0%-21.3% of the phenotypic variation. Two QTLs, namely, QGWpd.swust-3BS and QGWpd.swust-6DL, were detected for GW on chromosomes 3B and 6D, respectively. These QTLs explained 12.8%-14.6% and 10.8%-15.2% of the phenotypic variation, respectively. In addition, two QTLs, i.e., QLWRpd.swust-7AS.1 and QLWRpd.swust-7AS.2, were detected on chromosome 7A for the grain LWR, which explained 10.9%-11.6% and 11.6%-11.2% of the phenotypic variation, respectively. Another QTL, named QGNSpd-swust-6DS, was discovered on chromosome 6D, which determines the GNS and which accounted for 11.4%-13.8% of the phenotypic variation. Furthermore, five QTLs associated with PH were mapped on chromosomes 2D, 3A, 5A, 6B, and 7B. These QTLs were QPHpd.swust-2DL, QPHpd.swust-3AL, QPHpd.swust-5AL, QPHpd.swust-6BL, and QPHpd.swust-7BS, which accounted for 11.3%-19.3% of the phenotypic variation. Lastly, a QTL named QSLpd.swust-3AL, conferring SL, was detected on chromosome 3A and explained 16.1%-17.6% of the phenotypic variation. All of these QTLs were defined within the physical interval of the Chinese spring reference genome. Discussion The findings of this study have significant implications for the development of fine genetic maps, for genomic breeding, and for marker-assisted selection to enhance wheat grain yield.
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Affiliation(s)
- Liangqi Zhang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Yuqi Luo
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xiao Zhong
- Chongqing Banan District Agricultural Technology Promoting Station, Chongqing, China
| | - Guoyun Jia
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Hao Chen
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Yuqi Wang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Jianian Zhou
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Chunhua Ma
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Xin Li
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Kebing Huang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Suizhuang Yang
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
| | - Jianfeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shanxi, China
| | - Yong Ren
- Crop Characteristic Resources Creation and Utilization Key Laboratory of Sichuan Province, Mianyang Institute of Agricultural Science, Mianyang, Sichuan, China
| | - Lin Cai
- College of Tobacco Science of Guizhou University, Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou Key Lab of Agro-Bioengineering, Guiyang, China
| | - Xinli Zhou
- Wheat Research Institute, School of Life Sciences and Engineering, Southwest University of Science and Technology, Mianyang, Sichuan, China
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Wen T, Zhang X, Zhu J, Zhang S, Rhaman MS, Zeng W. A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize ( Zea mays L.). Front Plant Sci 2024; 15:1338086. [PMID: 38384753 PMCID: PMC10880447 DOI: 10.3389/fpls.2024.1338086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/05/2024] [Indexed: 02/23/2024]
Abstract
The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.
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Affiliation(s)
- Tingting Wen
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
- Seed Administration Station of Shandong Province, Jinan, China
| | - Xuefei Zhang
- Taian Daiyue District Bureau of Agriculture and Rural Affairs, Taian, China
| | - Jiaojiao Zhu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Susu Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
| | - Wei Zeng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, China
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Jiang J, Wang L, Fan G, Long Y, Lu X, Wang R, Liu H, Qiu X, Zeng D, Li Z. Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000. Plants (Basel) 2024; 13:179. [PMID: 38256733 PMCID: PMC10818613 DOI: 10.3390/plants13020179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
The morphological characteristics of the rice panicle play a pivotal role in influencing yield. In our research, we employed F2 and F2:3 populations derived from the high-yielding hybrid rice variety Chaoyou 1000. We screened 123 pairs of molecular markers, which were available, to construct the genetic linkage map. Subsequently, we assessed the panicle morphology traits of F2 populations in Lingshui County, Hainan Province, in 2017, and F2:3 populations in Hangzhou City, Zhejiang Province, in 2018. These two locations represent two types of ecology. Hangzhou's climate is characterized by high temperatures and humidity, while Lingshui's climate is characterized by a tropical monsoon climate. In total, 33 QTLs were identified, with eight of these being newly discovered, and two of them were consistently detected in two distinct environments. We identified fourteen QTL-by-environment interactions (QEs), which collectively explained 4.93% to 59.95% of the phenotypic variation. While most of the detected QTLs are consistent with the results of previous tests, the novel-detected QTLs will lay the foundation for rice yield increase and molecular breeding.
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Affiliation(s)
- Jing Jiang
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Li Wang
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Gucheng Fan
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Yu Long
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Xueli Lu
- China National Rice Research Institute, Hangzhou 310006, China (D.Z.)
| | - Run Wang
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Haiyang Liu
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Xianjin Qiu
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
| | - Dali Zeng
- China National Rice Research Institute, Hangzhou 310006, China (D.Z.)
| | - Zhixin Li
- Institute of Crop Genetics and Breeding, Yangtze University, Jingzhou 434025, China; (J.J.); (H.L.)
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Feng Y, Yang C, Zhang J, Qiao J, Wang B, Zhao Y. Construction of a High-Density Paulownia Genetic Map and QTL Mapping of Important Phenotypic Traits Based on Genome Assembly and Whole-Genome Resequencing. Int J Mol Sci 2023; 24:15647. [PMID: 37958630 PMCID: PMC10647314 DOI: 10.3390/ijms242115647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023] Open
Abstract
Quantitative trait locus (QTL) mapping based on a genetic map is a very effective method of marker-assisted selection in breeding, and whole-genome resequencing is one of the useful methods to obtain high-density genetic maps. In this study, the hybrid assembly of Illumina, PacBio, and chromatin interaction mapping data was used to construct high-quality chromosomal genome sequences of Paulownia fortunei, with a size of 476.82 Mb, a heterozygosity of 0.52%, and a contig and scaffold N50s of 7.81 Mb and 21.81 Mb, respectively. Twenty scaffolds with a total length of 437.72 Mb were assembled into 20 pseudochromosomes. Repeat sequences with a total length of 243.96 Mb accounted for 51.16% of the entire genome. In all, 26,903 protein-coding gene loci were identified, and 26,008 (96.67%) genes had conserved functional motifs. Further comparative genomics analysis preliminarily showed that the split of P. fortunei with Tectona grandis likely occurred 38.8 (33.3-45.1) million years ago. Whole-genome resequencing was used to construct a merged genetic map of 20 linkage groups, with 2993 bin markers (3,312,780 SNPs), a total length of 1675.14 cm, and an average marker interval of 0.56 cm. In total, 73 QTLs for important phenotypic traits were identified (19 major QTLs with phenotypic variation explained ≥ 10%), including 10 for the diameter at breast height, 7 for the main trunk height, and 56 for branch-related traits. These results not only enrich P. fortunei genomic data but also form a solid foundation for fine QTL mapping and key marker/gene mining of Paulownia, which is of great significance for the directed genetic improvement of these species.
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Affiliation(s)
- Yanzhi Feng
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Chaowei Yang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jiajia Zhang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Jie Qiao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Baoping Wang
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
| | - Yang Zhao
- Research Institute of Non-Timber Forestry, Chinese Academy of Forestry, Zhengzhou 450003, China; (Y.F.); (C.Y.); (J.Z.); (J.Q.)
- Key Laboratory of Non-Timber Forest Germplasm Enhancement & Utilization of National Forestry and Grassland Administration, Zhengzhou 450003, China
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Park HR, Seo JH, Kang BK, Kim JH, Heo SV, Choi MS, Ko JY, Kim CS. QTLs and Candidate Genes for Seed Protein Content in Two Recombinant Inbred Line Populations of Soybean. Plants (Basel) 2023; 12:3589. [PMID: 37896053 PMCID: PMC10610525 DOI: 10.3390/plants12203589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023]
Abstract
This study aimed to discover the quantitative trait loci (QTL) associated with a high seed protein content in soybean and unravel the potential candidate genes. We developed two recombinant inbred line populations: YS and SI, by crossing Saedanbaek (high protein) with YS2035-B-91-1-B-1 (low protein) and Saedanbaek with Ilmi (low protein), respectively, and evaluated the protein content for three consecutive years. Using single-nucleotide polymorphism (SNP)-marker-based linkage maps, four QTLs were located on chromosomes 15, 18, and 20 with high logarithm of odds values (5.9-55.0), contributing 5.5-66.0% phenotypic variance. In all three experimental years, qPSD20-1 and qPSD20-2 were stable and identified in overlapping positions in the YS and SI populations, respectively. Additionally, novel QTLs were identified on chromosomes 15 and 18. Considering the allelic sequence variation between parental lines, 28 annotated genes related to soybean seed protein-including starch, lipid, and fatty acid biosynthesis-related genes-were identified within the QTL regions. These genes could potentially affect protein accumulation during seed development, as well as sucrose and oil metabolism. Overall, this study offers insights into the genetic mechanisms underlying a high soybean protein content. The identified potential candidate genes can aid marker-assisted selection for developing soybean lines with an increased protein content.
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Affiliation(s)
| | - Jeong Hyun Seo
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang 50424, Republic of Korea; (H.R.P.); (B.K.K.); (J.H.K.); (S.V.H.); (M.S.C.); (J.Y.K.); (C.S.K.)
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Yue J, Krasovec M, Kazama Y, Zhang X, Xie W, Zhang S, Xu X, Kan B, Ming R, Filatov DA. The origin and evolution of sex chromosomes, revealed by sequencing of the Silene latifolia female genome. Curr Biol 2023:S0960-9822(23)00678-4. [PMID: 37290443 DOI: 10.1016/j.cub.2023.05.046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/07/2023] [Accepted: 05/19/2023] [Indexed: 06/10/2023]
Abstract
White campion (Silene latifolia, Caryophyllaceae) was the first vascular plant where sex chromosomes were discovered. This species is a classic model for studies on plant sex chromosomes due to presence of large, clearly distinguishable X and Y chromosomes that originated de novo about 11 million years ago (mya), but lack of genomic resources for this relatively large genome (∼2.8 Gb) remains a significant hurdle. Here we report S. latifolia female genome assembly integrated with sex-specific genetic maps of this species, focusing on sex chromosomes and their evolution. The analysis reveals a highly heterogeneous recombination landscape with strong reduction in recombination rate in the central parts of all chromosomes. Recombination on the X chromosome in female meiosis primarily occurs at the very ends, and over 85% of the X chromosome length is located in a massive (∼330 Mb) gene-poor, rarely recombining pericentromeric region (Xpr). The results indicate that the non-recombining region on the Y chromosome (NRY) initially evolved in a relatively small (∼15 Mb), actively recombining region at the end of the q-arm, possibly as a result of inversion on the nascent X chromosome. The NRY expanded about 6 mya via linkage between the Xpr and the sex-determining region, which may have been caused by expanding pericentromeric recombination suppression on the X chromosome. These findings shed light on the origin of sex chromosomes in S. latifolia and yield genomic resources to assist ongoing and future investigations into sex chromosome evolution.
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Affiliation(s)
- Jingjing Yue
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Marc Krasovec
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK; Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, 66650 Banyuls-sur-Mer, France
| | - Yusuke Kazama
- Department of Bioscience and Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-cho, Fukui 910-1195, Japan
| | - Xingtan Zhang
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China; Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Wangyang Xie
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Shencheng Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518100, China
| | - Xiuming Xu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361100, China
| | - Baolin Kan
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ray Ming
- Centre for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Dmitry A Filatov
- Department of Biology, University of Oxford, Oxford OX1 3RB, UK.
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8
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Liu F, Chen H, Yang L, You L, Ju J, Yang S, Wang X, Liu Z. QTL Mapping and Transcriptome Analysis Reveal Candidate Genes Regulating Seed Color in Brassica napus. Int J Mol Sci 2023; 24:ijms24119262. [PMID: 37298213 DOI: 10.3390/ijms24119262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Abstract
Yellow seeds are desirable in rapeseed breeding because of their higher oil content and better nutritional quality than black seeds. However, the underlying genes and formation mechanism of yellow seeds remain unclear. Here, a novel yellow-seeded rapeseed line (Huangaizao, HAZ) was crossed with a black-seeded rapeseed line (Zhongshuang11, ZS11) to construct a mapping population of 196 F2 individuals, based on which, a high-density genetic linkage map was constructed. This map, comprising 4174 bin markers, was 1618.33 cM in length and had an average distance of 0.39 cM between its adjacent markers. To assess the seed color of the F2 population, three methods (imaging, spectrophotometry, and visual scoring) were used and a common major quantitative trait locus (QTL) on chromosome A09, explaining 10.91-21.83% of the phenotypic variance, was detected. Another minor QTL, accounting for 6.19-6.69% of the phenotypic variance, was detected on chromosome C03, only by means of imaging and spectrophotometry. Furthermore, a dynamic analysis of the differential expressions between the parental lines showed that flavonoid biosynthesis-related genes were down-regulated in the yellow seed coats at 25 and 35 days after flowering. A coexpression network between the differentially expressed genes identified 17 candidate genes for the QTL intervals, including a flavonoid structure gene, novel4557 (BnaC03.TT4), and two transcription factor genes, namely, BnaA09G0616800ZS (BnaA09.NFYA8) and BnaC03G0060200ZS (BnaC03.NAC083), that may regulate flavonoid biosynthesis. Our study lays a foundation for further identifying the genes responsible for and understanding the regulatory mechanism of yellow seed formation in Brassica napus.
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Affiliation(s)
- Fangying Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Hao Chen
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Liu Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Liang You
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Jianye Ju
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Shujie Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Xiaolin Wang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhongsong Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
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9
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Li Y, Huo Y, Yang Y, Wang Z, Sun Y, Liu B, Wu X. Construction of a high-resolution genetic map and identification of single nucleotide polymorphism markers relevant to flower stalk height in onion. Front Plant Sci 2023; 14:1100691. [PMID: 36818885 PMCID: PMC9928573 DOI: 10.3389/fpls.2023.1100691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Onion (Allium cepa L., 2n=16) is an economically and nutritionally important vegetable crop worldwide. Construction of a high-resolution genetic map and map-based gene mining in onion have lagged behind other vegetable crops such as tomato and pepper. METHODS In this study, we constructed a high-resolution genetic map of onion using 321 F2 individuals from a cross between two double haploid lines DH-1×DH-17 and employing specific length amplified fragment (SLAF)-seq technology. The genetic map containing 10,584 polymorphic SLAFs with 21,250 single nucleotide polymorphism (SNP) markers and 8 linkage groups was developed for onion, which spanned 928.32 cM, with an average distance of 0.09 cM between adjacent markers. RESULTS Using this map, we carried out QTL mapping of Ms locus related to the male-fertile trait and reproduced previous mapping results, which proved that this map was of good quality. Then, four QTLs (located on LG2, LG5, and LG8) were detected for flower stalk height, explaining 26.60% of the phenotypic variance. Among them, we proposed that 20 SLAF markers (in three QTLs) of flower stalk height trait were effective favorable allelic variant markers associated with heterosis. DISCUSSION Overall, the genetic map was structured using SLAF-seq based on DH lines, and it is the highest-quality and highest-resolution linkage map of onion to date. It lays a foundation for the fine mapping and candidate gene identification of flower stalk height, and provides new insights into the developmental genetic mechanisms in onion breeding.
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Affiliation(s)
| | | | | | | | | | | | - Xiong Wu
- *Correspondence: Bingjiang Liu, ; Xiong Wu,
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10
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He RY, Yang T, Zheng JJ, Pan ZY, Chen Y, Zhou Y, Li XF, Li YZ, Iqbal MZ, Yang CY, He JM, Rong TZ, Tang QL. QTL Mapping and a Transcriptome Integrative Analysis Uncover the Candidate Genes That Control the Cold Tolerance of Maize Introgression Lines at the Seedling Stage. Int J Mol Sci 2023; 24. [PMID: 36768951 DOI: 10.3390/ijms24032629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/15/2023] [Accepted: 01/20/2023] [Indexed: 02/03/2023] Open
Abstract
Chilling injury owing to low temperatures severely affects the growth and development of maize (Zea mays.L) seedlings during the early and late spring seasons. The existing maize germplasm is deficient in the resources required to improve maize's ability to tolerate cold injury. Therefore, it is crucial to introduce and identify excellent gene/QTLs that confer cold tolerance to maize for sustainable crop production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant to cold and can be used to improve the cold tolerance of maize. In a previous study, a genetic bridge among maize that utilized Z. perennis and T. dactyloides was created and used to obtain a highly cold-tolerant maize introgression line (MIL)-IB030 by backcross breeding. In this study, two candidate genes that control relative electrical conductivity were located on MIL-IB030 by forward genetics combined with a weighted gene co-expression network analysis. The results of the phenotypic, genotypic, gene expression, and functional verification suggest that two candidate genes positively regulate cold tolerance in MIL-IB030 and could be used to improve the cold tolerance of cultivated maize. This study provides a workable route to introduce and mine excellent genes/QTLs to improve the cold tolerance of maize and also lays a theoretical and practical foundation to improve cultivated maize against low-temperature stress.
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11
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de la Herrán R, Hermida M, Rubiolo JA, Gómez-Garrido J, Cruz F, Robles F, Navajas-Pérez R, Blanco A, Villamayor PR, Torres D, Sánchez-Quinteiro P, Ramirez D, Rodríguez ME, Arias-Pérez A, Cross I, Duncan N, Martínez-Peña T, Riaza A, Millán A, De Rosa MC, Pirolli D, Gut M, Bouza C, Robledo D, Rebordinos L, Alioto T, Ruíz-Rejón C, Martínez P. A chromosome-level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex-determining gene in the flatfish Solea senegalensis. Mol Ecol Resour 2023; 23:886-904. [PMID: 36587276 DOI: 10.1111/1755-0998.13750] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 01/02/2023]
Abstract
Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and diversity of SD mechanisms. Here, we assembled the Solea senegalensis genome, a flatfish of great commercial value, into 82 contigs (614 Mb) combining long- and short-read sequencing, which were next scaffolded using a highly dense genetic map (28,838 markers, 21 linkage groups), representing 98.9% of the assembly. Further, we established the correspondence between the assembly and the 21 chromosomes by using BAC-FISH. Whole genome resequencing of six males and six females enabled the identification of 41 single nucleotide polymorphism variants in the follicle stimulating hormone receptor (fshr) consistent with an XX/XY SD system. The observed sex association was validated in a broader independent sample, providing a novel molecular sexing tool. The fshr gene displayed differential expression between male and female gonads from 86 days post-fertilization, when the gonad is still an undifferentiated primordium, concomitant with the activation of amh and cyp19a1a, testis and ovary marker genes, respectively, in males and females. The Y-linked fshr allele, which included 24 nonsynonymous variants and showed a highly divergent 3D protein structure, was overexpressed in males compared to the X-linked allele at all stages of gonadal differentiation. We hypothesize a mechanism hampering the action of the follicle stimulating hormone driving the undifferentiated gonad toward testis.
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Affiliation(s)
- Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Miguel Hermida
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Juan Andres Rubiolo
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Fernando Cruz
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Francisca Robles
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Andres Blanco
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Paula Rodriguez Villamayor
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Dorinda Torres
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Pablo Sánchez-Quinteiro
- Departamento de Anatomía, Producción Animal y Ciencias Clínicas Veterinarias Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Daniel Ramirez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Maria Esther Rodríguez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Alberto Arias-Pérez
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Ismael Cross
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Neil Duncan
- IRTA Sant Carles de la Rapita, Tarragona, Spain
| | | | - Ana Riaza
- Stolt Sea Farm SA, Departamento I+D, A Coruña, Spain
| | | | - M Cristina De Rosa
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Davide Pirolli
- Institute of Chemical Sciences and Technologies "Giulio Natta" (SCITEC) - CNR c/o Catholic University of Rome, Rome, Italy
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain
| | - Carmen Bouza
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, UK
| | - Laureana Rebordinos
- Departamento de Biomedicina, Biotecnología y Salud Pública CASEM - Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, Cádiz, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Carmelo Ruíz-Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Paulino Martínez
- Departamento de Zoología, Genética y Antropología Física; Facultad de Veterinaria, Universidade de Santiago de Compostela, Lugo, Spain
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12
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Hao N, Cao J, Wang C, Zhu Y, Du Y, Wu T. Understanding the molecular mechanism of leaf morphogenesis in vegetable crops conduces to breeding process. Front Plant Sci 2022; 13:971453. [PMID: 36570936 PMCID: PMC9773389 DOI: 10.3389/fpls.2022.971453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Leaf morphology can affect the development and yield of plants by regulating plant architecture and photosynthesis. Several factors can determine the final leaf morphology, including the leaf complexity, size, shape, and margin type, which suggests that leaf morphogenesis is a complex regulation network. The formation of diverse leaf morphology is precisely controlled by gene regulation on translation and transcription levels. To further reveal this, more and more genome data has been published for different kinds of vegetable crops and advanced genotyping approaches have also been applied to identify the causal genes for the target traits. Therefore, the studies on the molecular regulation of leaf morphogenesis in vegetable crops have also been largely improved. This review will summarize the progress on identified genes or regulatory mechanisms of leaf morphogenesis and development in vegetable crops. These identified markers can be applied for further molecular-assisted selection (MAS) in vegetable crops. Overall, the review will contribute to understanding the leaf morphology of different crops from the perspective of molecular regulation and shortening the breeding cycle for vegetable crops.
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Affiliation(s)
- Ning Hao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- College of Horticulture and Landscape, Northeast Agricultural University, Harbin, China
| | - Jiajian Cao
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Chunhua Wang
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Yipeng Zhu
- Guiyang Productivity Promotion Center, Guiyang Science and Technology Bureau, Guiyang, China
| | - Yalin Du
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
| | - Tao Wu
- College of Horticulture, Hunan Agricultural University, Changsha, China
- Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Changsha, China
- Engineering Research Center for Horticultural Crop Germplasm Creation and New Variety Breeding, Ministry of Education, Changsha, China
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13
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Roy CB, Goonetilleke SN, Joseph L, Krishnan A, Saha T, Kilian A, Mather DE. Analysis of Genetic Diversity and Resistance to Foliar Pathogens Based on Genotyping-by-Sequencing of a Para Rubber Diversity Panel and Progeny of an Interspecific Cross. Plants (Basel) 2022; 11:3418. [PMID: 36559531 PMCID: PMC9781018 DOI: 10.3390/plants11243418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/19/2022] [Accepted: 11/26/2022] [Indexed: 06/17/2023]
Abstract
Para rubber trees (Hevea brasiliensis) are the largest major source of natural rubber in the world. Its major pathogens are Phytophthora spp., Corynespora cassiicola, and Colletotrichum spp. A rubber diversity panel of 116 clones using over 12,000 single nucleotide polymorphisms (SNPs) from DArTSeq genotyping revealed clear phylogenetic differences in clones that originated from different geographical regions of the world. An integrated linkage map constructed with an F1 progeny of 86 from an interspecific cross between H. brasiliensis and H. benthamiana using 23,978 markers [10,323 SNPs and 13,655 SilicoDArTs] spanned 3947.83 cM with 0.83 cM average marker-interval. The genome scaffolds that were anchored to the linkage map, covering 1.44 Gb of H. brasiliensis reference genome, revealed a high level of collinearity between the genetic map and reference genome. Association analysis identified 12 SNPs significantly associated with the resistance against Phytophthora, Corynespora, and Colletotrichum in six linkage groups: 2, 6, 12, 14, 17, and 18. Kompetitive Allele-Specific PCR marker assays were developed for those 12 SNPs, screened with 178 individuals, and detected clear separation between two genotypes. Within the proximity to those SNPs, 41 potentially key genes that have previously been reported to associate with plant disease resistance were predicted with high confidence.
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Affiliation(s)
- C. Bindu Roy
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Shashi N. Goonetilleke
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia
| | - Limiya Joseph
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Anu Krishnan
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Thakurdas Saha
- Rubber Research Institute of India, Kottayam 686 009, India
| | - Andrzej Kilian
- Diversity Arrays Technology, Canberra, ACT 2617, Australia
| | - Diane E. Mather
- School of Agriculture, Food and Wine, Waite Research Institute, The University of Adelaide, Glen Osmond, SA 5064, Australia
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14
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Montanari S, Thomson S, Cordiner S, Günther CS, Miller P, Deng CH, McGhie T, Knäbel M, Foster T, Turner J, Chagné D, Espley R. High-density linkage map construction in an autotetraploid blueberry population and detection of quantitative trait loci for anthocyanin content. Front Plant Sci 2022; 13:965397. [PMID: 36247546 PMCID: PMC9555082 DOI: 10.3389/fpls.2022.965397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Highbush blueberry (Vaccinium corymbosum, 2n = 4x = 48) is the most cultivated type of blueberry, both in New Zealand and overseas. Its perceived nutritional value is conferred by phytonutrients, particularly anthocyanins. Identifying the genetic mechanisms that control the biosynthesis of these metabolites would enable faster development of cultivars with improved fruit qualities. Here, we used recently released tools for genetic mapping in autotetraploids to build a high-density linkage map in highbush blueberry and to detect quantitative trait loci (QTLs) for fruit anthocyanin content. Genotyping was performed by target sequencing, with ∼18,000 single nucleotide polymorphism (SNP) markers being mapped into 12 phased linkage groups (LGs). Fruits were harvested when ripe for two seasons and analyzed with high-performance liquid chromatography-mass spectrometry (HPLC-MS): 25 different anthocyanin compounds were identified and quantified. Two major QTLs that were stable across years were discovered, one on LG2 and one on LG4, and the underlying candidate genes were identified. Interestingly, the presence of anthocyanins containing acylated sugars appeared to be under strong genetic control. Information gained in this study will enable the design of molecular markers for marker-assisted selection and will help build a better understanding of the genetic control of anthocyanin biosynthesis in this crop.
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Affiliation(s)
- Sara Montanari
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - Susan Thomson
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Sarah Cordiner
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Catrin S. Günther
- The New Zealand Institute for Plant and Food Research Limited, Ruakura, New Zealand
| | - Poppy Miller
- The New Zealand Institute for Plant and Food Research Limited, Te Puke, New Zealand
| | - Cecilia H. Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
| | - Tony McGhie
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Mareike Knäbel
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Toshi Foster
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - Janice Turner
- The New Zealand Institute for Plant and Food Research Limited, Motueka, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Limited, Palmerston North, New Zealand
| | - Richard Espley
- The New Zealand Institute for Plant and Food Research Limited, Auckland, New Zealand
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15
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Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. Plant J 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
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Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
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16
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Liu X, Xu Z, Feng B, Zhou Q, Ji G, Guo S, Liao S, Lin D, Fan X, Wang T. Quantitative trait loci identification and breeding value estimation of grain weight-related traits based on a new wheat 50K single nucleotide polymorphism array-derived genetic map. Front Plant Sci 2022; 13:967432. [PMID: 36110352 PMCID: PMC9468616 DOI: 10.3389/fpls.2022.967432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 08/04/2022] [Indexed: 06/01/2023]
Abstract
Mining novel and less utilized thousand grain weight (TGW) related genes are useful for improving wheat yield. In this study, a recombinant inbred line population from a cross between Zhongkemai 138 (ZKM138, high TGW) and Chuanmai 44 (CM44, low TGW) was used to construct a new Wheat 50K SNP array-derived genetic map that spanned 1,936.59 cM and contained 4, 139 markers. Based on this map, ninety-one quantitative trait loci (QTL) were detected for eight grain-related traits in six environments. Among 58 QTLs, whose superior alleles were contributed by ZKM138, QTgw.cib-6A was a noticeable major stable QTL and was also highlighted by bulked segregant analysis with RNA sequencing (BSR-Seq). It had a pyramiding effect on TGW enhancement but no significant trade-off effect on grain number per spike or tiller number, with two other QTLs (QTgw.cib-2A.2 and QTgw.cib-6D), possibly explaining the excellent grain performance of ZKM138. After comparison with known loci, QTgw.cib-6A was deduced to be a novel locus that differed from nearby TaGW2 and TaBT1. Seven simple sequence repeat (SSR) and thirty-nine kompetitive allele-specific PCR (KASP) markers were finally developed to narrow the candidate interval of QTgw.cib-6A to 4.1 Mb. Only six genes in this interval were regarded as the most likely candidate genes. QTgw.cib-6A was further validated in different genetic backgrounds and presented 88.6% transmissibility of the ZKM138-genotype and a 16.4% increase of TGW in ZKM138 derivatives. And the geographic pattern of this locus revealed that its superior allele is present in only 6.47% of 433 Chinese modern wheat varieties, indicating its potential contribution to further high-yield breeding.
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Affiliation(s)
- Xiaofeng Liu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhibin Xu
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Bo Feng
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Qiang Zhou
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Guangsi Ji
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shaodan Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Simin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dian Lin
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Fan
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Tao Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
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17
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Prapas D, Scalone R, Lee J, Nurkowski KA, Bou‐assi S, Rieseberg L, Battlay P, Hodgins KA. Quantitative trait loci mapping reveals an oligogenic architecture of a rapidly adapting trait during the European invasion of common ragweed. Evol Appl 2022; 15:1249-1263. [PMID: 36051461 PMCID: PMC9423086 DOI: 10.1111/eva.13453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 06/05/2022] [Accepted: 06/30/2022] [Indexed: 01/09/2023] Open
Abstract
Biological invasions offer a unique opportunity to investigate evolution over contemporary timescales. Rapid adaptation to local climates during range expansion can be a major determinant of invasion success, yet fundamental questions remain about its genetic basis. This study sought to investigate the genetic basis of climate adaptation in invasive common ragweed (Ambrosia artemisiifolia). Flowering time adaptation is key to this annual species' invasion success, so much so that it has evolved repeated latitudinal clines in size and phenology across its native and introduced ranges despite high gene flow among populations. Here, we produced a high-density linkage map (4493 SNPs) and paired this with phenotypic data from an F2 mapping population (n = 336) to identify one major and two minor quantitative trait loci (QTL) underlying flowering time and height differentiation in this species. Within each QTL interval, several candidate flowering time genes were also identified. Notably, the major flowering time QTL detected in this study was found to overlap with a previously identified haploblock (putative inversion). Multiple genetic maps of this region identified evidence of suppressed recombination in specific genotypes, consistent with inversions. These discoveries support the expectation that a concentrated genetic architecture with fewer, larger, and more tightly linked alleles should underlie rapid local adaptation during invasion, particularly when divergently adapting populations experience high levels of gene flow.
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Affiliation(s)
- Diana Prapas
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Romain Scalone
- Department of Crop Production Ecology, Uppsala Ecology CenterSwedish University of Agricultural SciencesUppsalaSweden,Department of Grapevine BreedingHochschule Geisenheim UniversityGeisenheimGermany
| | - Jacqueline Lee
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kristin A. Nurkowski
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia,Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Sarah Bou‐assi
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Loren Rieseberg
- Department of Botany and Biodiversity Research CentreUniversity of British ColumbiaVancouverCanada
| | - Paul Battlay
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
| | - Kathryn A. Hodgins
- School of Biological SciencesMonash UniversityMelbourneVictoriaAustralia
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18
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Niu Y, Chen T, Zhao C, Guo C, Zhou M. Identification of QTL for Stem Traits in Wheat ( Triticum aestivum L.). Front Plant Sci 2022; 13:962253. [PMID: 35909739 PMCID: PMC9330363 DOI: 10.3389/fpls.2022.962253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
Lodging in wheat (Triticum aestivum L.) is a complicated phenomenon that is influenced by physiological, genetics, and external factors. It causes a great yield loss and reduces grain quality and mechanical harvesting efficiency. Lodging resistance is contributed by various traits, including increased stem strength. The aim of this study was to map quantitative trait loci (QTL) controlling stem strength-related features (the number of big vascular bundles, stem diameter, stem wall thickness) using a doubled haploid (DH) population derived from a cross between Baiqimai and Neixiang 5. Field experiments were conducted during 2020-2022, and glasshouse experiments were conducted during 2021-2022. Significant genetic variations were observed for all measured traits, and they were all highly heritable. Fifteen QTL for stem strength-related traits were identified on chromosomes 2D, 3A, 3B, 3D, 4B, 5A, 6B, 7A, and 7D, respectively, and 7 QTL for grain yield-related traits were identified on chromosomes 2B, 2D, 3D, 4B, 7A, and 7B, respectively. The superior allele of the major QTL for the number of big vascular bundle (VB) was independent of plant height (PH), making it possible to improve stem strength without a trade-off of PH, thus improving lodging resistance. VB also showed positive correlations with some of the yield components. The result will be useful for molecular marker-assisted selection (MAS) for high stem strength and high yield potential.
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Affiliation(s)
- Yanan Niu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Tianxiao Chen
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Chenchen Zhao
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Ce Guo
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
- College of Agronomy, Shanxi Agricultural University, Taigu, China
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19
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Abstract
Genetic mutation and recombination are driving the evolution of SARS-CoV-2, leaving many genetic imprints which could be utilized to track the evolutionary pathway of SARS-CoV-2 and explore the relationships among variants. Here, we constructed a complete genetic map, showing the explicit evolutionary relationship among all SARS-CoV-2 variants including 58 groups and 46 recombination types identified from 3,392,553 sequences, which enables us to keep well informed of the evolution of SARS-CoV-2 and quickly determine the parents of novel variants. We found that the 5' and 3' of the spike and nucleoprotein genes have high frequencies to form the recombination junctions and that the RBD region in S gene is always exchanged as a whole. Although these recombinants did not show advantages in community transmission, it is necessary to keep a wary eye on the novel genetic events, in particular, the mutants with mutations on spike and recombinants with exchanged moieties on spike gene.
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Affiliation(s)
- Luyao Qin
- Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Jing Meng
- Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Xiao Ding
- Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
| | - Taijiao Jiang
- Institute of Systems Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
- Suzhou Institute of Systems Medicine, Suzhou, China
- Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
- Guangzhou Laboratory, Guangzhou, China
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20
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Wu J, Mao L, Tao J, Wang X, Zhang H, Xin M, Shang Y, Zhang Y, Zhang G, Zhao Z, Wang Y, Cui M, Wei L, Song X, Sun X. Dynamic Quantitative Trait Loci Mapping for Plant Height in Recombinant Inbred Line Population of Upland Cotton. Front Plant Sci 2022; 13:914140. [PMID: 35769288 PMCID: PMC9235862 DOI: 10.3389/fpls.2022.914140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/06/2022] [Indexed: 06/15/2023]
Abstract
Plant height (PH) is a key plant architecture trait for improving the biological productivity of cotton. Ideal PH of cotton is conducive to lodging resistance and mechanized harvesting. To detect quantitative trait loci (QTL) and candidate genes of PH in cotton, a genetic map was constructed with a recombinant inbred line (RIL) population of upland cotton. PH phenotype data under nine environments and three best linear unbiased predictions (BLUPs) were used for QTL analyses. Based on restriction-site-associated DNA sequence (RAD-seq), the genetic map contained 5,850 single-nucleotide polymorphism (SNP) markers, covering 2,747.12 cM with an average genetic distance of 0.47 cM. Thirty-seven unconditional QTL explaining 1.03-12.50% of phenotypic variance, including four major QTL and seven stable QTL, were identified. Twenty-eight conditional QTL explaining 3.27-28.87% of phenotypic variance, including 1 major QTL, were identified. Importantly, five QTL, including 4 stable QTL, were both unconditional and conditional QTL. Among the 60 PH QTL (including 39 newly identified), none of them were involved in the whole period of PH growth, indicating that QTL related to cotton PH development have dynamic expression characteristics. Based on the functional annotation of Arabidopsis homologous genes and transcriptome data of upland cotton TM-1, 14 candidate genes were predicted within 10 QTL. Our research provides valuable information for understanding the genetic mechanism of PH development, which also increases the economic production of cotton.
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Affiliation(s)
- Jing Wu
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Lili Mao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Jincai Tao
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest Agriculture and Forestry University, Xianyang, China
| | - Xiuxiu Wang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Haijun Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Ming Xin
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Yongqi Shang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Yanan Zhang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Guihua Zhang
- Heze Academy of Agricultural Sciences, Heze, China
| | | | - Yiming Wang
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Mingshuo Cui
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Liming Wei
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Xianliang Song
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
| | - Xuezhen Sun
- State Key Laboratory of Crop Biology, Agronomy College, Shandong Agricultural University, Taian, China
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21
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Jiang X, Yang T, Zhang F, Yang X, Yang C, He F, Long R, Gao T, Jiang Y, Yang Q, Wang Z, Kang J. RAD-Seq-Based High-Density Linkage Maps Construction and Quantitative Trait Loci Mapping of Flowering Time Trait in Alfalfa ( Medicago sativa L.). Front Plant Sci 2022; 13:899681. [PMID: 35720570 PMCID: PMC9199863 DOI: 10.3389/fpls.2022.899681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 04/25/2022] [Indexed: 06/15/2023]
Abstract
Alfalfa (Medicago sativa L.) is a perennial forage crop known as the "Queen of Forages." To dissect the genetic mechanism of flowering time (FT) in alfalfa, high-density linkage maps were constructed for both parents of an F1 mapping population derived from a cross between Cangzhou (P1) and ZhongmuNO.1 (P2), consisting of 150 progenies. The FT showed a transgressive segregation pattern in the mapping population. A total of 13,773 single-nucleotide polymorphism markers was obtained by using restriction-site associated DNA sequencing and distributed on 64 linkage groups, with a total length of 3,780.49 and 4,113.45 cM and an average marker interval of 0.58 and 0.59 cM for P1 and P2 parent, respectively. Quantitative trait loci (QTL) analyses were performed using the least square means of each year as well as the best linear unbiased prediction values across 4 years. Sixteen QTLs for FT were detected for P1 and 22 QTLs for P2, accounting for 1.40-16.04% of FT variation. RNA-Seq analysis at three flowering stages identified 5,039, 7,058, and 7,996 genes that were differentially expressed between two parents, respectively. Based on QTL mapping, DEGs analysis, and functional annotation, seven candidate genes associated with flowering time were finally detected. This study discovered QTLs and candidate genes for alfalfa FT, making it a useful resource for breeding studies on this essential crop.
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Affiliation(s)
- Xueqian Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tianhui Yang
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Fan Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xijiang Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Changfu Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fei He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ruicai Long
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ting Gao
- Institute of Animal Science, Ningxia Academy of Agricultural and Forestry Sciences, Yinchuan, China
| | - Yiwei Jiang
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
| | - Qingchuan Yang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junmei Kang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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22
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Janousek B, Gogela R, Bacovsky V, Renner SS. The evolution of huge Y chromosomes in Coccinia grandis and its sister, Coccinia schimperi. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210294. [PMID: 35306898 PMCID: PMC8935295 DOI: 10.1098/rstb.2021.0294] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Microscopically dimorphic sex chromosomes in plants are rare, reducing our ability to study them. One difficulty has been the paucity of cultivatable species pairs for cytogenetic, genomic and experimental work. Here, we study the newly recognized sisters Coccinia grandis and Coccinia schimperi, both with large Y chromosomes as we here show for Co. schimperi. We built genetic maps for male and female Co. grandis using a full-sibling family, inferred gene sex-linkage, and, with Co. schimperi transcriptome data, tested whether X- and Y-alleles group by species or by sex. Most sex-linked genes for which we could include outgroups grouped the X- and Y-alleles by species, but some 10% instead grouped the two species' X-alleles. There was no relationship between XY synonymous-site divergences in these genes and gene position on the non-recombining part of the X, suggesting recombination arrest shortly before or after species divergence, here dated to about 3.6 Ma. Coccinia grandis and Co. schimperi are the species pair with the most heteromorphic sex chromosomes in vascular plants (the condition in their sister remains unknown), and future work could use them to study mechanisms of Y chromosome enlargement and parallel degeneration, or to test Haldane's rule about lower hybrid fitness in the heterogametic sex. This article is part of the theme issue 'Sex determination and sex chromosome evolution in land plants'.
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Affiliation(s)
- Bohuslav Janousek
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
| | - Roman Gogela
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
| | - Vaclav Bacovsky
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 61265 Brno, Czech Republic
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO, USA
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23
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Boopathi NM, Tiwari GJ, Jena SN, Nandhini K, Sri Subalakhshmi VKI, Shyamala P, Joshi B, Premalatha N, Rajeswari S. Identification of Stable and Multiple Environment Interaction QTLs and Candidate Genes for Fiber Productive Traits Under Irrigated and Water Stress Conditions Using Intraspecific RILs of Gossypium hirsutum var. MCU5 X TCH1218. Front Plant Sci 2022; 13:851504. [PMID: 35519814 PMCID: PMC9062235 DOI: 10.3389/fpls.2022.851504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Cotton productivity under water-stressed conditions is controlled by multiple quantitative trait loci (QTL). Enhancement of these productivity traits under water deficit stress is crucial for the genetic improvement of upland cotton, Gossypium hirsutum. In the present study, we constructed a genetic map with 504 single nucleotide polymorphisms (SNPs) covering a total span length of 4,416 cM with an average inter-marker distance of 8.76 cM. A total of 181 intra-specific recombinant inbred lines (RILs) were derived from a cross between G. hirsutum var. MCU5 and TCH1218 were used. Although 2,457 polymorphic SNPs were detected between the parents using the CottonSNP50K assay, only 504 SNPs were found to be useful for the construction of the genetic map. In the SNP genotyping, a large number of SNPs showed either >20% missing data, duplication, or segregation distortion. However, the mapped SNPs of this study showed collinearity with the physical map of the reference genome (G. hirsutum var.TM-1), indicating that there was no chromosomal rearrangement within the studied mapping population. RILs were evaluated under multi-environments and seasons for which the phenotypic data were acquired. A total of 53 QTL controlling plant height (PH), number of sympodial branches, boll number (BN), and boll weight (BW) were dissected by QTL analysis under irrigated and water stress conditions. Additionally, it was found that nine QTL hot spots not only co-localized for more than one investigated trait but were also stable with major QTL, i.e., with > 10% of phenotypic variation. One QTL hotspot on chromosome 22 flanked by AX-182254626-AX-182264770 with a span length of 89.4 cM co-localized with seven major and stable QTL linked to a number of sympodial branches both under irrigated and water stress conditions. In addition, putative candidate genes associated with water stress in the QTL hotspots were identified. Besides, few QTL from the hotspots were previously reported across various genetic architects in cotton validating the potential applications of these identified QTL for cotton breeding and improvement. Thus, the major and stable QTL identified in the present study would improve the cotton productivity under water-limited environments through marker-assisted selection.
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Affiliation(s)
| | - Gopal Ji Tiwari
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
| | - Satya Narayan Jena
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
| | - Kemparaj Nandhini
- Department of Cotton, CPBG, Tamil Nadu Agricultural University, Coimbatore, India
| | | | - Pilla Shyamala
- Department of Plant Biotechnology, CPMB&B, Tamil Nadu Agricultural University, Coimbatore, India
| | - Babita Joshi
- Plant Molecular Genetics Laboratory, CSIR-National Botanical Research Institute, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | | | - S. Rajeswari
- Department of Cotton, CPBG, Tamil Nadu Agricultural University, Coimbatore, India
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24
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Wei K, Wang X, Hao X, Qian Y, Li X, Xu L, Ruan L, Wang Y, Zhang Y, Bai P, Li Q, Aktar S, Hu X, Zheng G, Wang L, Liu B, He W, Cheng H, Wang L. Development of a genome-wide 200K SNP array and its application for high-density genetic mapping and origin analysis of Camellia sinensis. Plant Biotechnol J 2022; 20:414-416. [PMID: 34873805 PMCID: PMC8882773 DOI: 10.1111/pbi.13761] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/02/2021] [Accepted: 11/30/2021] [Indexed: 05/07/2023]
Affiliation(s)
- Kang Wei
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Xinyuan Hao
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Yinhong Qian
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Xin Li
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Liyi Xu
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Li Ruan
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Yongxin Wang
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Yazhen Zhang
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Peixian Bai
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Qiang Li
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Shirin Aktar
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Xili Hu
- Jinyun Agricultrual BureauJinyunChina
| | | | - Liubin Wang
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Benying Liu
- Tea Research InstituteYunnan Academy of Agricultural SciencesMenghaiChina
| | - Weizhong He
- Lishui Academy of Agricultural SciencesLishuiChina
| | - Hao Cheng
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
| | - Liyuan Wang
- Key Laboratory of Tea Biology and Resources UtilizationMinistry of AgricultureNational Center for Tea ImprovementTea Research Institute Chinese Academy of Agricultural Sciences (TRICAAS)HangzhouChina
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Cui Y, Fan B, Xu X, Sheng S, Xu Y, Wang X. A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia. Front Genet 2022; 12:802738. [PMID: 35132310 PMCID: PMC8817757 DOI: 10.3389/fgene.2021.802738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/13/2021] [Indexed: 11/13/2022] Open
Abstract
The gardenia is a traditional medicinal horticultural plant in China, but its molecular genetic research has been largely hysteretic. Here, we constructed an F1 population with 200 true hybrid individuals. Using the genotyping-by-sequencing method, a high-density sex-average genetic map was generated that contained 4,249 SNPs with a total length of 1956.28 cM and an average genetic distance of 0.46 cM. We developed 17 SNP-based Kompetitive Allele-Specific PCR markers and found that 15 SNPs were successfully genotyped, of which 13 single-nucleotide polymorphism genotypings of 96 F1 individuals showed genotypes consistent with GBS-mined genotypes. A genomic collinearity analysis between gardenia and the Rubiaceae species Coffea arabica, Coffea canephora and Ophiorrhiza pumila showed the relativity strong conservation of LG11 with NC_039,919.1, HG974438.1 and Bliw01000011.1, respectively. Lastly, a quantitative trait loci analysis at three phenotyping time points (2019, 2020, and 2021) yielded 18 QTLs for growth-related traits and 31 QTLs for leaf-related traits, of which qBSBN7-1, qCD8 and qLNP2-1 could be repeatably detected. Five QTL regions (qCD8 and qSBD8, qBSBN7 and qSI7, qCD4-1 and qLLLS4, qLNP10 and qSLWS10-2, qSBD10 and qLLLS10) with potential pleiotropic effects were also observed. This study provides novel insight into molecular genetic research and could be helpful for further gene cloning and marker-assisted selection for early growth and development traits in the gardenia.
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Affiliation(s)
- Yang Cui
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Baolian Fan
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Xu Xu
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Shasha Sheng
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, China
| | - Xiaoyun Wang
- Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, Nanchang, China
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26
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Sawada C, Moreau C, Robinson GHJ, Steuernagel B, Wingen LU, Cheema J, Sizer-Coverdale E, Lloyd D, Domoney C, Ellis N. An Integrated Linkage Map of Three Recombinant Inbred Populations of Pea ( Pisum sativum L.). Genes (Basel) 2022; 13:196. [PMID: 35205241 PMCID: PMC8871737 DOI: 10.3390/genes13020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 11/17/2022] Open
Abstract
Biparental recombinant inbred line (RIL) populations are sets of genetically stable lines and have a simple population structure that facilitates the dissection of the genetics of interesting traits. On the other hand, populations derived from multiparent intercrosses combine both greater diversity and higher numbers of recombination events than RILs. Here, we describe a simple population structure: a three-way recombinant inbred population combination. This structure was easy to produce and was a compromise between biparental and multiparent populations. We show that this structure had advantages when analyzing cultivar crosses, and could achieve a mapping resolution of a few genes.
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Affiliation(s)
- Chie Sawada
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
| | - Carol Moreau
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
| | - Gabriel H. J. Robinson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
| | - Burkhard Steuernagel
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
| | - Luzie U. Wingen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
| | - Jitender Cheema
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
| | - Ellen Sizer-Coverdale
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EB, UK;
| | - David Lloyd
- Germinal Horizon, Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth SY23 3EB, UK;
| | - Claire Domoney
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
| | - Noel Ellis
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich NR4 7UH, UK; (C.S.); (C.M.); (G.H.J.R.); (B.S.); (L.U.W.); (J.C.); (C.D.)
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Liu X, Yang L, Wang J, Wang Y, Guo Z, Li Q, Yang J, Wu Y, Chen L, Teng Z, Liu D, Liu D, Guo K, Zhang Z. Analyzing Quantitative Trait Loci for Fiber Quality and Yield-Related Traits From a Recombinant Inbred Line Population With Gossypium hirsutum Race palmeri as One Parent. Front Plant Sci 2022; 12:817748. [PMID: 35046989 PMCID: PMC8763314 DOI: 10.3389/fpls.2021.817748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Fiber quality and yield-related traits are important agronomic traits in cotton breeding. To detect the genetic basis of fiber quality and yield related traits, a recombinant inbred line (RIL) population consisting of 182 lines was established from a cross between Gossypium hirsutum cultivar CCRI35 and G. hirsutum race palmeri accession TX-832. The RIL population was deeply genotyped using SLAF-seq and was phenotyped in six environments. A high-density genetic linkage map with 15,765 SNP markers and 153 SSR markers was constructed, with an average distance of 0.30 cM between adjacent markers. A total of 210 fiber quality quantitative trait loci (QTLs) and 73 yield-related QTLs were identified. Of the detected QTLs, 62 fiber quality QTLs and 10 yield-related QTLs were stable across multiple environments. Twelve and twenty QTL clusters were detected on the At and Dt subgenome, respectively. Twenty-three major QTL clusters were further validated through associated analysis and five candidate genes of four stable fiber quality QTLs were identified. This study revealed elite loci influencing fiber quality and yield and significant phenotypic selection regions during G. hirsutum domestication, and set a stage for future utilization of molecular marker assisted breeding in cotton breeding programs.
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Li F, Han Z, Qiao W, Wang J, Song Y, Cui Y, Li J, Ge J, Lou D, Fan W, Li D, Nong B, Zhang Z, Cheng Y, Zhang L, Zheng X, Yang Q. High-Quality Genomes and High-Density Genetic Map Facilitate the Identification of Genes From a Weedy Rice. Front Plant Sci 2021; 12:775051. [PMID: 34868173 PMCID: PMC8639688 DOI: 10.3389/fpls.2021.775051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Genes have been lost or weakened from cultivated rice during rice domestication and breeding. Weedy rice (Oryza sativa f. spontanea) is usually recognized as the progeny between cultivated rice and wild rice and is also known to harbor an gene pool for rice breeding. Therefore, identifying genes from weedy rice germplasms is an important way to break the bottleneck of rice breeding. To discover genes from weedy rice germplasms, we constructed a genetic map based on w-hole-genome sequencing of a F2 population derived from the cross between LM8 and a cultivated rice variety. We further identified 31 QTLs associated with 12 important agronomic traits and revealed that ORUFILM03g000095 gene may play an important role in grain length regulation and participate in grain formation. To clarify the genomic characteristics from weedy rice germplasms of LM8, we generated a high-quality genome assembly using single-molecule sequencing, Bionano optical mapping, and Hi-C technologies. The genome harbored a total size of 375.8 Mb, a scaffold N50 of 24.1 Mb, and originated approximately 0.32 million years ago (Mya) and was more closely related to Oryza sativa ssp. japonica. and contained 672 unique genes. It is related to the formation of grain shape, heading date and tillering. This study generated a high-quality reference genome of weedy rice and high-density genetic map that would benefit the analysis of genome evolution for related species and suggested an effective way to identify genes related to important agronomic traits for further rice breeding.
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Affiliation(s)
- Fei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhenyun Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weihua Qiao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junrui Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine Sciences and Biotechnology, Guangxi University for Nationalities, Nanning, China
| | - Yue Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yongxia Cui
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- School of Clinical Medicine, Southwest Medical University, Luzhou, China
| | - Jiaqi Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Little Berry Research Room, Liaoning Institute of Fruit Science, Yingkou, China
| | - Jinyue Ge
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danjing Lou
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Weiya Fan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Danting Li
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Baoxuan Nong
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zongqiong Zhang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yunlian Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Kim MS, Lee T, Baek J, Kim JH, Kim C, Jeong SC. Genome assembly of the popular Korean soybean cultivar Hwangkeum. G3 (Bethesda) 2021; 11:jkab272. [PMID: 34568925 PMCID: PMC8496230 DOI: 10.1093/g3journal/jkab272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/27/2021] [Indexed: 01/01/2023]
Abstract
Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated as containing 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence (Wm82.a2.v1) revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel subfamilies, we found that soybean contains four clearly separated subfamilies of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.
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Affiliation(s)
- Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
- Plant Immunity Research Center, Interdisciplinary Program in Agricultural Genomics, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Taeyoung Lee
- Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
| | - Jeonghun Baek
- Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
| | - Ji Hong Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Changhoon Kim
- Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
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30
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van Eeden G, Uren C, van der Spuy G, Tromp G, Möller M. Local ancestry inference in heterogeneous populations-Are recent recombination events more relevant? Brief Bioinform 2021; 22:6337894. [PMID: 34343255 DOI: 10.1093/bib/bbab300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/29/2021] [Accepted: 07/14/2021] [Indexed: 12/11/2022] Open
Abstract
To date, numerous software tools have been developed to infer recombination maps. Many of these software tools infer the recombination rate from linkage disequilibrium, and therefore they infer recombination many generations into the past. Other recently developed methods rely on the inference of recent recombination events to determine the recombination rate, such as identity by descent- and local ancestry inference (LAI)-based tools. Methods that mainly use recent recombination events to infer the recombination rate might be more relevant for certain analyses like LAI. We therefore describe a protocol for creating high-resolution, population-specific recombination maps using methods that mainly use recent recombination events and a method that uses recent and distant recombination events for recombination rate inference. Subsequently, we compared the effect of using maps inferred by these two paradigms on LAI accuracy.
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Affiliation(s)
| | | | - Gian van der Spuy
- Department of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
| | - Gerard Tromp
- South African Tuberculosis Bioinformatics Initiative (SATBBI), South Africa
| | - Marlo Möller
- Department of Molecular Biology and Human Genetics, Stellenbosch University, South Africa
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Shirasawa K, Kobayashi N, Nakatsuka A, Ohta H, Isobe S. Whole-genome sequencing and analysis of two azaleas, Rhododendron ripense and Rhododendron kiyosumense. DNA Res 2021; 28:6325020. [PMID: 34289022 PMCID: PMC8435550 DOI: 10.1093/dnares/dsab010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 11/26/2022] Open
Abstract
To enhance the genomics and genetics of azalea, the whole-genome sequences of two species of Rhododendron were determined and analysed in this study: Rhododendron ripense, the cytoplasmic donor and ancestral species of large-flowered and evergreen azalea cultivars; and Rhododendron kiyosumense, a native of Chiba prefecture (Japan) seldomly bred and cultivated. A chromosome-level genome sequence assembly of R. ripense was constructed by single-molecule real-time sequencing and genetic mapping, while the genome sequence of R. kiyosumense was assembled using the single-tube long fragment read sequencing technology. The R. ripense genome assembly contained 319 contigs (506.7 Mb; N50 length: 2.5 Mb) and was assigned to the genetic map to establish 13 pseudomolecule sequences. On the other hand, the genome of R. kiyosumense was assembled into 32,308 contigs (601.9 Mb; N50 length: 245.7 kb). A total of 34,606 genes were predicted in the R. ripense genome, while 35,785 flower and 48,041 leaf transcript isoforms were identified in R. kiyosumense through Iso-Seq analysis. Overall, the genome sequence information generated in this study enhances our understanding of genome evolution in the Ericales and reveals the phylogenetic relationship of closely related species. This information will also facilitate the development of phenotypically attractive azalea cultivars.
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Affiliation(s)
- Kenta Shirasawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Nobuo Kobayashi
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane 690-8504, Japan
| | - Akira Nakatsuka
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane 690-8504, Japan
| | - Hideya Ohta
- Faculty of Life and Environmental Science, Shimane University, Matsue, Shimane 690-8504, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
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Foulongne-Oriol M, Taskent O, Kües U, Sonnenberg ASM, van Peer AF, Giraud T. Mating-Type Locus Organization and Mating-Type Chromosome Differentiation in the Bipolar Edible Button Mushroom Agaricus bisporus. Genes (Basel) 2021; 12:1079. [PMID: 34356095 PMCID: PMC8305134 DOI: 10.3390/genes12071079] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 12/20/2022] Open
Abstract
In heterothallic basidiomycete fungi, sexual compatibility is restricted by mating types, typically controlled by two loci: PR, encoding pheromone precursors and pheromone receptors, and HD, encoding two types of homeodomain transcription factors. We analysed the single mating-type locus of the commercial button mushroom variety, Agaricus bisporus var. bisporus, and of the related variety burnettii. We identified the location of the mating-type locus using genetic map and genome information, corresponding to the HD locus, the PR locus having lost its mating-type role. We found the mip1 and β-fg genes flanking the HD genes as in several Agaricomycetes, two copies of the β-fg gene, an additional HD2 copy in the reference genome of A. bisporus var. bisporus and an additional HD1 copy in the reference genome of A. bisporus var. burnettii. We detected a 140 kb-long inversion between mating types in an A. bisporus var. burnettii heterokaryon, trapping the HD genes, the mip1 gene and fragments of additional genes. The two varieties had islands of transposable elements at the mating-type locus, spanning 35 kb in the A. bisporus var. burnettii reference genome. Linkage analyses showed a region with low recombination in the mating-type locus region in the A. bisporus var. burnettii variety. We found high differentiation between β-fg alleles in both varieties, indicating an ancient event of recombination suppression, followed more recently by a suppression of recombination at the mip1 gene through the inversion in A. bisporus var. burnettii and a suppression of recombination across whole chromosomes in A. bisporus var. bisporus, constituting stepwise recombination suppression as in many other mating-type chromosomes and sex chromosomes.
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Affiliation(s)
| | - Ozgur Taskent
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France;
| | - Ursula Kües
- Molecular Wood Biotechnology and Technical Mycology, Goettingen Center for Molecular Biosciences (GZMB), Büsgen-Institute, University of Goettingen, Büsgenweg 2, 37077 Goettingen, Germany;
| | - Anton S. M. Sonnenberg
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.S.M.S.); (A.F.v.P.)
| | - Arend F. van Peer
- Plant Breeding, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; (A.S.M.S.); (A.F.v.P.)
| | - Tatiana Giraud
- Ecologie Systématique Evolution, Bâtiment 360, CNRS, AgroParisTech, Université Paris-Saclay, 91400 Orsay, France;
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Zhang S, Yu Z, Qi X, Wang Z, Zheng Y, Ren H, Liang S, Zheng X. Construction of a High-Density Genetic Map and Identification of Leaf Trait-Related QTLs in Chinese Bayberry ( Myrica rubra). Front Plant Sci 2021; 12:675855. [PMID: 34194452 PMCID: PMC8238045 DOI: 10.3389/fpls.2021.675855] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/18/2021] [Indexed: 06/13/2023]
Abstract
Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.
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Affiliation(s)
| | | | - Xingjiang Qi
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Lv D, Zhang C, Yv R, Yao J, Wu J, Song X, Jian J, Song P, Zhang Z, Han D, Sun D. Utilization of a Wheat50K SNP Microarray-Derived High-Density Genetic Map for QTL Mapping of Plant Height and Grain Traits in Wheat. Plants (Basel) 2021; 10:1167. [PMID: 34201388 DOI: 10.3390/plants10061167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 11/22/2022]
Abstract
Plant height is significantly correlated with grain traits, which is a component of wheat yield. The purpose of this study is to investigate the main quantitative trait loci (QTLs) that control plant height and grain-related traits in multiple environments. In this study, we constructed a high-density genetic linkage map using the Wheat50K SNP Array to map QTLs for these traits in 198 recombinant inbred lines (RILs). The two ends of the chromosome were identified as recombination-rich areas in all chromosomes except chromosome 1B. Both the genetic map and the physical map showed a significant correlation, with a correlation coefficient between 0.63 and 0.99. However, there was almost no recombination between 1RS and 1BS. In terms of plant height, 1RS contributed to the reduction of plant height by 3.43 cm. In terms of grain length, 1RS contributed to the elongation of grain by 0.11 mm. A total of 43 QTLs were identified, including eight QTLs for plant height (PH), 11 QTLs for thousand grain weight (TGW), 15 QTLs for grain length (GL), and nine QTLs for grain width (GW), which explained 1.36–33.08% of the phenotypic variation. Seven were environment-stable QTLs, including two loci (Qph.nwafu-4B and Qph.nwafu-4D) that determined plant height. The explanation rates of phenotypic variation were 7.39–12.26% and 20.11–27.08%, respectively. One QTL, Qtgw.nwafu-4B, which influenced TGW, showed an explanation rate of 3.43–6.85% for phenotypic variation. Two co-segregating KASP markers were developed, and the physical locations corresponding to KASP_AX-109316968 and KASP_AX-109519968 were 25.888344 MB and 25.847691 MB, respectively. Qph.nwafu-4B, controlling plant height, and Qtgw.nwafu-4B, controlling TGW, had an obvious linkage relationship, with a distance of 7–8 cM. Breeding is based on molecular markers that control plant height and thousand-grain weight by selecting strains with low plant height and large grain weight. Another QTL, Qgw.nwafu-4D, which determined grain width, had an explanation rate of 3.43–6.85%. Three loci that affected grain length were Qgl.nwafu-5A, Qgl.nwafu-5D.2, and Qgl.nwafu-6B, illustrating the explanation rates of phenotypic variation as 6.72–9.59%, 5.62–7.75%, and 6.68–10.73%, respectively. Two QTL clusters were identified on chromosomes 4B and 4D.
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Xu YY, Liu SR, Gan ZM, Zeng RF, Zhang JZ, Hu CG. High-Density Genetic Map Construction and Identification of QTLs Controlling Leaf Abscission Trait in Poncirus trifoliata. Int J Mol Sci 2021; 22:ijms22115723. [PMID: 34072027 PMCID: PMC8198561 DOI: 10.3390/ijms22115723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/06/2021] [Accepted: 05/24/2021] [Indexed: 11/16/2022] Open
Abstract
A high-density genetic linkage map is essential for genetic and genomic studies including QTL mapping, genome assembly, and comparative genomic analysis. Here, we constructed a citrus high-density linkage map using SSR and SNP markers, which are evenly distributed across the citrus genome. The integrated linkage map contains 4163 markers with an average distance of 1.12 cM. The female and male linkage maps contain 1478 and 2976 markers with genetic lengths of 1093.90 cM and 1227.03 cM, respectively. Meanwhile, a genetic map comparison demonstrates that the linear order of common markers is highly conserved between the clementine mandarin and Poncirus trifoliata. Based on this high-density integrated citrus genetic map and two years of deciduous phenotypic data, two loci conferring leaf abscission phenotypic variation were detected on scaffold 1 (including 36 genes) and scaffold 8 (including 107 genes) using association analysis. Moreover, the expression patterns of 30 candidate genes were investigated under cold stress conditions because cold temperature is closely linked with the deciduous trait. The developed high-density genetic map will facilitate QTL mapping and genomic studies, and the localization of the leaf abscission deciduous trait will be valuable for understanding the mechanism of this deciduous trait and citrus breeding.
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Affiliation(s)
| | | | | | | | - Jin-Zhi Zhang
- Correspondence: (J.-Z.Z.); (C.-G.H.); Tel.: +86-27-8728-2010 (J.-Z.Z. & C.-G.H.)
| | - Chun-Gen Hu
- Correspondence: (J.-Z.Z.); (C.-G.H.); Tel.: +86-27-8728-2010 (J.-Z.Z. & C.-G.H.)
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Vitale P, Fania F, Esposito S, Pecorella I, Pecchioni N, Palombieri S, Sestili F, Lafiandra D, Taranto F, De Vita P. QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents. Genes (Basel) 2021; 12:genes12040604. [PMID: 33923933 PMCID: PMC8074140 DOI: 10.3390/genes12040604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/15/2021] [Accepted: 04/17/2021] [Indexed: 01/20/2023] Open
Abstract
Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.
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Affiliation(s)
- Paolo Vitale
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Fabio Fania
- Department of Agriculture, Food, Natural Science, Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy; (P.V.); (F.F.)
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Ivano Pecorella
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Nicola Pecchioni
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
| | - Samuela Palombieri
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, 01100 Viterbo, Italy; (S.P.); (F.S.); (D.L.)
| | - Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 80055 Portici, Italy
- Correspondence: (F.T.); (P.D.V.)
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA—Council for Agricultural Research and Economics, 71122 Foggia, Italy; (S.E.); (I.P.); (N.P.)
- Correspondence: (F.T.); (P.D.V.)
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Abstract
Despite its important biological role, the evolution of recombination rates remains relatively poorly characterized. This owes, in part, to the lack of high-quality genomic resources to address this question across diverse species. Humans and our closest evolutionary relatives, anthropoid apes, have remained a major focus of large-scale sequencing efforts, and thus recombination rate variation has been comparatively well studied in this group-with earlier work revealing a conservation at the broad- but not the fine-scale. However, in order to better understand the nature of this variation, and the time scales on which substantial modifications occur, it is necessary to take a broader phylogenetic perspective. I here present the first fine-scale genetic map for vervet monkeys based on whole-genome population genetic data from ten individuals and perform a series of comparative analyses with the great apes. The results reveal a number of striking features. First, owing to strong positive correlations with diversity and weak negative correlations with divergence, analyses suggest a dominant role for purifying and background selection in shaping patterns of variation in this species. Second, results support a generally reduced broad-scale recombination rate compared with the great apes, as well as a narrower fraction of the genome in which the majority of recombination events are observed to occur. Taken together, this data set highlights the great necessity of future research to identify genomic features and quantify evolutionary processes that are driving these rate changes across primates.
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Affiliation(s)
- Susanne P Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ
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Qi X, Ogden EL, Bostan H, Sargent DJ, Ward J, Gilbert J, Iorizzo M, Rowland LJ. High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population. Front Plant Sci 2021; 12:692628. [PMID: 34234801 PMCID: PMC8256855 DOI: 10.3389/fpls.2021.692628] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/24/2021] [Indexed: 05/11/2023]
Abstract
Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85-20) with the parent W85-23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.
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Affiliation(s)
- Xinpeng Qi
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Elizabeth L. Ogden
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Hamed Bostan
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | | | - Judson Ward
- Driscoll’s Inc., Watsonville, CA, United States
| | | | - Massimo Iorizzo
- Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC, United States
| | - Lisa J. Rowland
- Genetic Improvement of Fruits and Vegetables Laboratory, Beltsville Agricultural Research Center-West, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
- *Correspondence: Lisa J. Rowland, ;
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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,
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Pandey MK, Gangurde SS, Sharma V, Pattanashetti SK, Naidu GK, Faye I, Hamidou F, Desmae H, Kane NA, Yuan M, Vadez V, Nigam SN, Varshney RK. Improved Genetic Map Identified Major QTLs for Drought Tolerance- and Iron Deficiency Tolerance-Related Traits in Groundnut. Genes (Basel) 2020; 12:37. [PMID: 33396649 DOI: 10.3390/genes12010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/21/2020] [Accepted: 12/25/2020] [Indexed: 12/01/2022] Open
Abstract
A deep understanding of the genetic control of drought tolerance and iron deficiency tolerance is essential to hasten the process of developing improved varieties with higher tolerance through genomics-assisted breeding. In this context, an improved genetic map with 1205 loci was developed spanning 2598.3 cM with an average 2.2 cM distance between loci in the recombinant inbred line (TAG 24 × ICGV 86031) population using high-density 58K single nucleotide polymorphism (SNP) “Axiom_Arachis” array. Quantitative trait locus (QTL) analysis was performed using extensive phenotyping data generated for 20 drought tolerance- and two iron deficiency tolerance-related traits from eight seasons (2004–2015) at two locations in India, one in Niger, and one in Senegal. The genome-wide QTL discovery analysis identified 19 major main-effect QTLs with 10.0–33.9% phenotypic variation explained (PVE) for drought tolerance- and iron deficiency tolerance- related traits. Major main-effect QTLs were detected for haulm weight (20.1% PVE), SCMR (soil plant analytical development (SPAD) chlorophyll meter reading, 22.4% PVE), and visual chlorosis rate (33.9% PVE). Several important candidate genes encoding glycosyl hydrolases; malate dehydrogenases; microtubule-associated proteins; and transcription factors such as MADS-box, basic helix-loop-helix (bHLH), NAM, ATAF, and CUC (NAC), and myeloblastosis (MYB) were identified underlying these QTL regions. The putative function of these genes indicated their possible involvement in plant growth, development of seed and pod, and photosynthesis under drought or iron deficiency conditions in groundnut. These genomic regions and candidate genes, after validation, may be useful to develop molecular markers for deploying genomics-assisted breeding for enhancing groundnut yield under drought stress and iron-deficient soil conditions.
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Catchen J, Amores A, Bassham S. Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny. G3 (Bethesda) 2020; 10:4115-28. [PMID: 32912931 DOI: 10.1534/g3.120.401485] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a “chromonome”. We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.
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Peng M, Zeng D, Zhu W, Chen X, Yang C, Liu Q, Li Q, Wang H, Liu H, Liang J, Lin Y, Chen X, Zhao Y. Construction of a High-Density Genetic Map and Identification of Quantitative Trait Loci for Nitrite Tolerance in the Pacific White Shrimp ( Litopenaeus vannamei). Front Genet 2020; 11:571880. [PMID: 33193676 PMCID: PMC7541944 DOI: 10.3389/fgene.2020.571880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/07/2020] [Indexed: 11/25/2022] Open
Abstract
Nitrite is a major environmental toxin in aquaculture systems that disrupts multiple physiological functions in aquatic animals. Although nitrite tolerance in shrimp is closely related to successful industrial production, few genetic studies of this trait are available. In this study, we constructed a high-density genetic map of Litopenaeus vannamei with 17,242 single nucleotide polymorphism markers spanning 6,828.06 centimorgans (cM), with an average distance of 0.4 cM between adjacent markers on 44 linkage groups (LGs). Using this genetic map, we identified two markers associated with nitrite tolerance. We then sequenced the transcriptomes of the most nitrite-tolerant and nitrite-sensitive individuals from each of four genetically distinct L. vannamei families (LV-I–4). We found 2,002, 1,983, 1,954, and 1,867 differentially expressed genes in families LV-1, LV-2, LV-3, and LV-4, respectively. By integrating QTL and transcriptomics analyses, we identified a candidate gene associated with nitrite tolerance. This gene was annotated as solute carrier family 26 member 6 (SLC26A6). RNA interference (RNAi) analysis demonstrated that SLC26A6 was critical for nitrite tolerance in L. vannamei. The present study increases our understanding of the molecular mechanisms underlying nitrite tolerance in shrimp and provides a basis for molecular-marker-assisted shrimp breeding.
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Affiliation(s)
- Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Weilin Zhu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, China
| | - Hong Liu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery, Huazhong Agriculture University, Wuhan, China
| | - Jingzhen Liang
- Life Science Research Institute, Guangxi University, Nanning, China
| | - Yong Lin
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Xiaohan Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning, China
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Abstract
Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the F2 and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F2 family. Accessions showed a moderate level of diversity (mean He = 0.341) and evidence of inbreeding (mean F = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers.
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Affiliation(s)
- Joanne A Labate
- Plant Genetic Resources Unit, United States Department of Agriculture, Agricultural Research Service, 630 W. North St., Geneva, NY 14456, USA
| | - Jeffrey C Glaubitz
- Institute of Biotechnology, 526 Campus Rd., Cornell University, Ithaca, NY 14853, USA
| | - Michael J Havey
- Vegetable Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, 1575 Linden Drive, Madison, WI 53706, USA
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Samuk K, Manzano-Winkler B, Ritz KR, Noor MAF. Natural Selection Shapes Variation in Genome-wide Recombination Rate in Drosophila pseudoobscura. Curr Biol 2020; 30:1517-1528.e6. [PMID: 32275873 DOI: 10.1016/j.cub.2020.03.053] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/16/2019] [Accepted: 03/20/2020] [Indexed: 12/30/2022]
Abstract
While recombination is widely recognized to be a key modulator of numerous evolutionary phenomena, we have a poor understanding of how recombination rate itself varies and evolves within a species. Here, we performed a comprehensive study of recombination rate (rate of meiotic crossing over) in two natural populations of Drosophila pseudoobscura from Utah and Arizona, USA. We used an amplicon sequencing approach to obtain high-quality genotypes in approximately 8,000 individual backcrossed offspring (17 mapping populations with roughly 530 individuals each), for which we then quantified crossovers. Interestingly, variation in recombination rate within and between populations largely manifested as differences in genome-wide recombination rate rather than remodeling of the local recombination landscape. Comparing populations, we discovered individuals from the Utah population displayed on average 8% higher crossover rates than the Arizona population, a statistically significant difference. Using a QST-FST analysis, we found that this difference in crossover rate was dramatically higher than expected under neutrality, indicating that this difference may have been driven by natural selection. Finally, using a combination of short- and long-read whole-genome sequencing, we found no significant association between crossover rate and structural variation at the 200-400 kb scale. Our results demonstrate that (1) there is abundant variation in genome-wide crossover rate in natural populations, (2) at the 200-400 kb scale, recombination rate appears to vary largely genome-wide, rather than in specific intervals, and (3) interpopulation differences in recombination rate may be the result of local adaptation.
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Affiliation(s)
- Kieran Samuk
- Department of Biology, Duke University, Durham, NC 27708, USA.
| | | | - Kathryn R Ritz
- Department of Biology, Duke University, Durham, NC 27708, USA
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Takehana Y, Zahm M, Cabau C, Klopp C, Roques C, Bouchez O, Donnadieu C, Barrachina C, Journot L, Kawaguchi M, Yasumasu S, Ansai S, Naruse K, Inoue K, Shinzato C, Schartl M, Guiguen Y, Herpin A. Genome Sequence of the Euryhaline Javafish Medaka, Oryzias javanicus: A Small Aquarium Fish Model for Studies on Adaptation to Salinity. G3 (Bethesda) 2020; 10:907-15. [PMID: 31988161 DOI: 10.1534/g3.119.400725] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The genus Oryzias consists of 35 medaka-fish species each exhibiting various ecological, morphological and physiological peculiarities and adaptations. Beyond of being a comprehensive phylogenetic group for studying intra-genus evolution of several traits like sex determination, behavior, morphology or adaptation through comparative genomic approaches, all medaka species share many advantages of experimental model organisms including small size and short generation time, transparent embryos and genome editing tools for reverse and forward genetic studies. The Java medaka, Oryzias javanicus, is one of the two species of medaka perfectly adapted for living in brackish/sea-waters. Being an important component of the mangrove ecosystem, O. javanicus is also used as a valuable marine test-fish for ecotoxicology studies. Here, we sequenced and assembled the whole genome of O. javanicus, and anticipate this resource will be catalytic for a wide range of comparative genomic, phylogenetic and functional studies. Complementary sequencing approaches including long-read technology and data integration with a genetic map allowed the final assembly of 908 Mbp of the O. javanicus genome. Further analyses estimate that the O. javanicus genome contains 33% of repeat sequences and has a heterozygosity of 0.96%. The achieved draft assembly contains 525 scaffolds with a total length of 809.7 Mbp, a N50 of 6,3 Mbp and a L50 of 37 scaffolds. We identified 21454 predicted transcripts for a total transcriptome size of 57, 146, 583 bps. We provide here a high-quality chromosome scale draft genome assembly of the euryhaline Javafish medaka (321 scaffolds anchored on 24 chromosomes (representing 97.7% of the total bases)), and give emphasis on the evolutionary adaptation to salinity.
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Peñalba JV, Deng Y, Fang Q, Joseph L, Moritz C, Cockburn A. Genome of an iconic Australian bird: High-quality assembly and linkage map of the superb fairy-wren (Malurus cyaneus). Mol Ecol Resour 2020; 20:560-578. [PMID: 31821695 DOI: 10.1111/1755-0998.13124] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/09/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022]
Abstract
The superb fairy-wren, Malurus cyaneus, is one of the most iconic Australian passerine species. This species belongs to an endemic Australasian clade, Meliphagides, which diversified early in the evolution of the oscine passerines. Today, the oscine passerines comprise almost half of all avian species diversity. Despite the rapid increase of available bird genome assemblies, this part of the avian tree has not yet been represented by a high-quality reference. To rectify that, we present the first high-quality genome assembly of a Meliphagides representative: the superb fairy-wren. We combined Illumina shotgun and mate-pair sequences, PacBio long-reads, and a genetic linkage map from an intensively sampled pedigree of a wild population to generate this genome assembly. Of the final assembled 1.07-Gb genome, 975 Mb (90.4%) was anchored onto 25 pseudochromosomes resulting in a final superscaffold N50 of 68.11 Mb. This high-quality bird genome assembly is one of only a handful which is also accompanied by a genetic map and recombination landscape. In comparison to other pedigree-based bird genetic maps, we find that the fairy-wren genetic map more closely resembles those of Taeniopygia guttata and Parus major maps, unlike the Ficedula albicollis map which more closely resembles that of Gallus gallus. Lastly, we also provide a predictive gene and repeat annotation of the genome assembly. This new high-quality, annotated genome assembly will be an invaluable resource not only regarding the superb fairy-wren species and relatives but also broadly across the avian tree by providing a novel reference point for comparative genomic analyses.
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Affiliation(s)
- Joshua V Peñalba
- Division of Evolutionary Biology, Ludwig Maximilian University of Munich, Munich, Germany
| | | | - Qi Fang
- BGI-Shenzhen, Shenzhen, China
| | - Leo Joseph
- Australian National Wildlife Collection, CSIRO National Research Collections, Australia, Canberra, ACT, Australia
| | - Craig Moritz
- Centre for Biodiversity Analysis, Acton, ACT, Australia.,Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
| | - Andrew Cockburn
- Division of Ecology and Evolution, Australian National University, Acton, ACT, Australia
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Wen Y, Fang Y, Hu P, Tan Y, Wang Y, Hou L, Deng X, Wu H, Zhu L, Zhu L, Chen G, Zeng D, Guo L, Zhang G, Gao Z, Dong G, Ren D, Shen L, Zhang Q, Xue D, Qian Q, Hu J. Construction of a High-Density Genetic Map Based on SLAF Markers and QTL Analysis of Leaf Size in Rice. Front Plant Sci 2020; 11:1143. [PMID: 32849702 PMCID: PMC7411225 DOI: 10.3389/fpls.2020.01143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/14/2020] [Indexed: 05/02/2023]
Abstract
Leaf shape is an important agronomic trait for constructing an ideal plant type in rice, and high-density genetic map is facilitative in improving accuracy and efficiency for quantitative trait loci (QTL) analysis of leaf trait. In this study, a high-density genetic map contained 10,760 specific length amplified fragment sequencing (SLAF) markers was established based on 149 recombinant inbred lines (RILs) derived from the cross between Rekuangeng (RKG) and Taizhong1 (TN1), which exhibited 1,613.59 cM map distance with an average interval of 0.17 cM. A total of 24 QTLs were detected and explained the phenotypic variance ranged from 9% to 33.8% related to the leaf morphology across two areas. Among them, one uncloned major QTL qTLLW1 (qTLL1 and qTLLW1) involved in regulating leaf length and leaf width with max 33.8% and 22.5% phenotypic variance respectively was located on chromosome 1, and another major locus qTLW4 affecting leaf width accounted for max 25.3% phenotypic variance was mapped on chromosome 4. Fine mapping and qRT-PCR expression analysis indicated that qTLW4 may be allelic to NAL1 (Narrow leaf 1) gene.
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Affiliation(s)
- Yi Wen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
| | - Yunxia Fang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Peng Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yiqing Tan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yueying Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Linlin Hou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xuemei Deng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Hao Wu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lixin Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guang Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Deyong Ren
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qiang Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dawei Xue
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Rice Research Institute of Shenyang Agricultural University/Key Laboratory of Northern Japonica Rice Genetics and Breeding, Ministry of Education and Liaoning Province, Shenyang, China
- *Correspondence: Qian Qian, ; Jiang Hu,
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- *Correspondence: Qian Qian, ; Jiang Hu,
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Luo X, Xu L, Wang Y, Dong J, Chen Y, Tang M, Fan L, Zhu Y, Liu L. An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.). Plant Biotechnol J 2020; 18:274-286. [PMID: 31218798 PMCID: PMC6920339 DOI: 10.1111/pbi.13195] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/19/2023]
Abstract
High-density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high-resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra-high-density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole-genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish.
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Affiliation(s)
- Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Guizhou Institute of BiotechnologyGuizhou Academy of Agricultural SciencesGuiyangChina
| | | | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yuelin Zhu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
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Czyczyło-Mysza IM, Cyganek K, Dziurka K, Quarrie S, Skrzypek E, Marcińska I, Myśków B, Dziurka M, Warchoł M, Kapłoniak K, Bocianowski J. Genetic Parameters and QTLs for Total Phenolic Content and Yield of Wheat Mapping Population of CSDH Lines under Drought Stress. Int J Mol Sci 2019; 20:E6064. [PMID: 31805731 PMCID: PMC6929150 DOI: 10.3390/ijms20236064] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/29/2019] [Accepted: 11/30/2019] [Indexed: 01/29/2023] Open
Abstract
A doubled haploid population of 94 lines from the Chinese Spring × SQ1 wheat cross (CSDH) was used to evaluate additive and epistatic gene action effects on total phenolic content, grain yield of the main stem, grain number per plant, thousand grain weight, and dry weight per plant at harvest based on phenotypic and genotypic observations of CSDH lines. These traits were evaluated under moderate and severe drought stress and compared with well-watered plants. Plants were grown in pots in an open-sided greenhouse. Genetic parameters, such as additive and epistatic effects, affecting total phenolic content, were estimated for eight year-by-drought combinations. Twenty-one markers showed a significant additive effect on total phenolic content in all eight year-by-drought combinations. These markers were located on chromosomes: 1A, 1B, 2A, 2B, 2D, 3A, 3B, 3D, 4A, and 4D. A region on 4AL with a stable QTL controlling the phenolic content, confirmed by various statistical methods is particularly noteworthy. In all years and treatments, three markers significantly linked to QTLs have been identified for both phenols and yield. Thirteen markers were coincident with candidate genes. Our results indicated the importance of both additive and epistatic gene effects on total phenolic content in eight year-by-drought combinations.
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Affiliation(s)
- Ilona Mieczysława Czyczyło-Mysza
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Katarzyna Cyganek
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Kinga Dziurka
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Steve Quarrie
- Faculty of Biology, Belgrade University, Studentski trg 16, 11000 Belgrade, Serbia;
| | - Edyta Skrzypek
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Izabela Marcińska
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Beata Myśków
- Department of Plant Genetics, Breeding and Biotechnology, West-Pomeranian University of Technology, Szczecin ul. Słowackiego 17, 71-434 Szczecin, Poland;
| | - Michał Dziurka
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Marzena Warchoł
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Kamila Kapłoniak
- Polish Academy of Sciences, The Franciszek Górski Institute of Plant Physiology, 30-239 Kraków, Niezapominajek 21, Poland; (K.C.); (K.D.); (E.S.); (I.M.); (M.D.); (M.W.); (K.K.)
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland;
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50
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Wang Z, Zhang Z, Tang H, Zhang Q, Zhou G, Li X. High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill. Front Plant Sci 2019; 10:1424. [PMID: 31824522 PMCID: PMC6882864 DOI: 10.3389/fpls.2019.01424] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 10/14/2019] [Indexed: 05/23/2023]
Abstract
The Chinese jujube (Ziziphus jujuba Mill., 2n = 2x = 24), one of the most popular fruit trees in Asia, is widely cultivated and utilized in China, where it is traditionally consumed as both a fresh and dried food resource. A high-density genetic map can provide the necessary framework for quantitative trait loci (QTL) analyses and map-based gene cloning and molecular breeding. In this study, we constructed a new high-density genetic linkage map via a genotyping-by-sequencing approach. For the consensus linkage map, a total of 3,792 markers spanning 2,167.5 cM were mapped onto 12 linkage groups, with an average marker interval distance of 0.358 cM. The genetic map anchored 301 Mb (85.7%) of scaffolds from the sequenced Z. jujuba "Junzao" genome. Based on this genetic map, 30 potential QTLs were detected, including 27 QTLs for leaf traits and 3 QTLs for needling length. This high-density genetic map and the identified QTLs for relevant agronomic traits lay the groundwork for functional genetic mapping, map-based cloning, and marker-assisted selection in jujube.
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Affiliation(s)
- Zhongtang Wang
- College of Forestry, Northwest A&F University, Yangling, China
- Country Shandong Institute of Pomology, Taian, China
| | - Zhong Zhang
- College of Forestry, Northwest A&F University, Yangling, China
- Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Northwest A&F University, Yangling, China
| | - Haixia Tang
- Country Shandong Institute of Pomology, Taian, China
| | - Qiong Zhang
- Country Shandong Institute of Pomology, Taian, China
| | | | - Xingang Li
- College of Forestry, Northwest A&F University, Yangling, China
- Research Centre for Jujube Engineering and Technology of State Forestry and Grassland Administration, Northwest A&F University, Yangling, China
- Key Comprehensive Laboratory of Forestry of Shaanxi Province, Northwest A&F University, Yangling, China
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