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Ortega F, Hill T, Van Deynze A, Garcia-Llanos A, Walker S. Identification of QTLs involved in destemming and fruit quality for mechanical harvesting of New Mexico pod-type green chile. FRONTIERS IN PLANT SCIENCE 2024; 15:1357986. [PMID: 39011303 PMCID: PMC11246910 DOI: 10.3389/fpls.2024.1357986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 06/12/2024] [Indexed: 07/17/2024]
Abstract
Introduction Domestic production of pepper (Capsicum spp.) is shrinking while demand within the US is growing. Lack of availability and cost of labor often present an obstacle for domestic producers both practically and economically. As a result, switching to harvesting peppers mechanically is anticipated as a key strategy to help domestic producers compete in the international market. Mechanical harvest efficiency can be improved through breeding. One important trait that mechanical harvest compatible material should have is an easy destemming trait: low force separation of the pedicel and calyx from the fruit. Methods To detect the genetic sources underlying a novel easy destemming trait for the purpose of future breeding efforts in New Mexico pod-type green chile, we performed QTL analysis on three F2:F3 populations, coming from three New Mexico pod-type varieties: 'NuMex Odyssey,' 'NuMex Iliad,' and 'NuMex Joe E. Parker,' each crossed with a parent with an easy destemming trait: MUC14. Genotyping was done through genotyping by sequencing (GBS) and phenotyping was done for destemming and fruit trait measurements. Correlations between measurements were found through the R package hmisc and QTL analysis was done through R/qtl. Results A strong relationship was seen between destemming and aspects of fruit morphology, particularly, destemming force and fruit width (Pearson's correlation coefficient r=0.75). Major QTLs for destemming and fruit size were discovered. Of these, the largest destemming force QTLs for all populations (PVE=34.5-69.9%) were on chromosome 10, and in two populations QTLs for destemming force were found on chromosome 3 (Percent Variance Explained (PVE)=10.7-18.8%). Fruit size-related QTLs in all populations colocalized in these same areas on chromosomes 3 and 10. Discussion This suggests that fruit shape may be genetically linked to destemming, and breeders interested in selecting for easy destemming pepper will also have to pay attention to fruit size and shape.
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Affiliation(s)
- Franchesca Ortega
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Theresa Hill
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
| | - Allen Van Deynze
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
| | - Armando Garcia-Llanos
- Seed Biotechnology Center, University of California, Davis, Davis, CA, United States
| | - Stephanie Walker
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
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Fu G, Yu S, Wu K, Yang M, Altaf MA, Wu Z, Deng Q, Lu X, Fu H, Wang Z, Cheng S. Genome-wide association study and candidate gene identification for agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. Sci Rep 2024; 14:14691. [PMID: 38926509 PMCID: PMC11208541 DOI: 10.1038/s41598-024-65332-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 06/19/2024] [Indexed: 06/28/2024] Open
Abstract
Pepper agronomic traits serve as pivotal indicators for characterizing germplasm attributes and correlations. It is important to study differential genotypic variation through phenotypic differences of target traits. Whole genome resequencing was used to sequence the whole genome among different individuals of species with known reference genomes and annotations, and based on this, differential analyses of individuals or populations were carried out to identify SNPs for agronomic traits related to pepper. This study conducted a genome-wide association study encompassing 26 key agronomic traits in 182 upward-growing fruits of C. frutescens and C. annuum. The population structure (phylogenetics, population structure, population principal component analysis, genetic relationship) and linkage disequilibrium analysis were realized to ensure the accuracy and reliability of GWAS results, and the optimal statistical model was determined. A total of 929 SNPs significantly associated with 26 agronomic traits, were identified, alongside the detection of 519 candidate genes within 100 kb region adjacent to these SNPs. Additionally, through gene annotation and expression pattern scrutiny, genes such as GAUT1, COP10, and DDB1 correlated with fruit traits in Capsicum frutescens and Capsicum annuum were validated via qRT-PCR. In the CH20 (Capsicum annuum) and YB-4 (Capsicum frutescens) cultivars, GAUT1 and COP10 were cloned with cDNA lengths of 1065 bp and 561 bp, respectively, exhibiting only a small number of single nucleotide variations and nucleotide deletions. This validation provides a robust reference for molecular marker-assisted breeding of pepper agronomic traits, offering both genetic resources and theoretical foundations for future endeavors in molecular marker-assisted breeding for pepper.
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Affiliation(s)
- Genying Fu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shuang Yu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Kun Wu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Mengxian Yang
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Muhammad Ahsan Altaf
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Zhuo Wu
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Qin Deng
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Xu Lu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Huizhen Fu
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
| | - Zhiwei Wang
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Shanhan Cheng
- Key Laboratory for Quality Regulation of Horticultural Crops of Hainan Province, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China.
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China.
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Kaur N, Lozada DN, Bhatta M, Barchenger DW, Khokhar ES, Nourbakhsh SS, Sanogo S. Insights into the genetic architecture of Phytophthora capsici root rot resistance in chile pepper (Capsicum spp.) from multi-locus genome-wide association study. BMC PLANT BIOLOGY 2024; 24:416. [PMID: 38760676 PMCID: PMC11100198 DOI: 10.1186/s12870-024-05097-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 05/02/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Phytophthora root rot, a major constraint in chile pepper production worldwide, is caused by the soil-borne oomycete, Phytophthora capsici. This study aimed to detect significant regions in the Capsicum genome linked to Phytophthora root rot resistance using a panel consisting of 157 Capsicum spp. genotypes. Multi-locus genome wide association study (GWAS) was conducted using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS). Individual plants were separately inoculated with P. capsici isolates, 'PWB-185', 'PWB-186', and '6347', at the 4-8 leaf stage and were scored for disease symptoms up to 14-days post-inoculation. Disease scores were used to calculate disease parameters including disease severity index percentage, percent of resistant plants, area under disease progress curve, and estimated marginal means for each genotype. RESULTS Most of the genotypes displayed root rot symptoms, whereas five accessions were completely resistant to all the isolates and displayed no symptoms of infection. A total of 55,117 SNP markers derived from GBS were used to perform multi-locus GWAS which identified 330 significant SNP markers associated with disease resistance. Of these, 56 SNP markers distributed across all the 12 chromosomes were common across the isolates, indicating association with more durable resistance. Candidate genes including nucleotide-binding site leucine-rich repeat (NBS-LRR), systemic acquired resistance (SAR8.2), and receptor-like kinase (RLKs), were identified within 0.5 Mb of the associated markers. CONCLUSIONS Results will be used to improve resistance to Phytophthora root rot in chile pepper by the development of Kompetitive allele-specific markers (KASP®) for marker validation, genomewide selection, and marker-assisted breeding.
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Affiliation(s)
- Navdeep Kaur
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Current address: Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Dennis N Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, 88003, USA.
| | | | | | - Ehtisham S Khokhar
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Seyed Shahabeddin Nourbakhsh
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Soum Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, 88003, USA
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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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Adhikari P, Siddique MI, Louws FJ, Panthee DR. Identification of quantitative trait loci associated with bacterial spot race T4 resistance in intra-specific populations of tomato (Solanum lycopersicum L.). PLoS One 2023; 18:e0295551. [PMID: 38079392 PMCID: PMC10712892 DOI: 10.1371/journal.pone.0295551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Bacterial spot of tomato is a serious disease caused by at least four species and four races of Xanthomonas- X. euvesicatoria (race T1), X. vesicatoria (race T2), X. perforans (race T3 and T4), and X. gardneri, with X. perforans race T4 being predominant in the southeast USA. Practical management of this disease is challenging because of the need for more effective chemicals and commercially resistant cultivars. Identification of genetic resistance is the first step to developing a disease-resistant variety. The objective of this study was to identify quantitative trait loci (QTL) conferring resistance to race T4 in two independent recombinant inbred lines (RILs) populations NC 10204 (intra-specific) and NC 13666 (interspecific) developed by crossing NC 30P x NC22L-1(2008) and NC 1CELBR x PI 270443, respectively. Seven QTLs on chromosomes 2, 6, 7, 11, and 12 were identified in NC 10204. The QTL on chromosome 6 explained the highest percentage of phenotypic variance (up to 21.3%), followed by the QTL on chromosome 12 (up to 8.2%). On the other hand, the QTLs on chromosomes 1, 3, 4, 6, 7, 8, 9, and 11 were detected in NC 13666. The QTLs on chromosomes 6, 7, and 11 were co-located in NC 10204 and NC 13666 populations. The donor of the resistance associated with these QTL in NC 10204 is a released breeding line with superior horticultural traits. Therefore, both the donor parent and the QTL information will be useful in tomato breeding programs as there will be minimal linkage drag associated with the bacterial spot resistance.
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Affiliation(s)
- Pragya Adhikari
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
- Bayer Crop Science, Huxley, Iowa, United States of America
| | - Muhammad Irfan Siddique
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
| | - Frank J. Louws
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
- Department of Horticultural Science and Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, United States of America
| | - Dilip R. Panthee
- Department of Horticultural Science, Mountain Horticultural Crops Research and Extension Center, North Carolina State University, Mills River, North Carolina, United States of America
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6
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Liu Z, Sun H, Zhang Y, Du M, Xiang J, Li X, Chang Y, Sun J, Cheng X, Xiong M, Zhao Z, Liu E. Mining the candidate genes of rice panicle traits via a genome-wide association study. Front Genet 2023; 14:1239550. [PMID: 37732315 PMCID: PMC10507276 DOI: 10.3389/fgene.2023.1239550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023] Open
Abstract
Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei, China
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Lopez-Moreno H, Basurto-Garduño AC, Torres-Meraz MA, Diaz-Valenzuela E, Arellano-Arciniega S, Zalapa J, Sawers RJH, Cibrián-Jaramillo A, Diaz-Garcia L. Genetic analysis and QTL mapping of domestication-related traits in chili pepper ( Capsicum annuum L .). Front Genet 2023; 14:1101401. [PMID: 37255716 PMCID: PMC10225550 DOI: 10.3389/fgene.2023.1101401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/31/2023] [Indexed: 06/01/2023] Open
Abstract
Chili pepper (Capsicum annuum L.) is one of the oldest and most phenotypically diverse pre-Columbian crops of the Americas. Despite the abundance of genetic resources, the use of wild germplasm and landraces in chili pepper breeding is limited. A better understanding of the evolutionary history in chili peppers, particularly in the context of traits of agronomic interest, can contribute to future improvement and conservation of genetic resources. In this study, an F2:3 mapping population derived from a cross between a C. annuum wild accession (Chiltepin) and a cultivated variety (Puya) was used to identify genomic regions associated with 19 domestication and agronomic traits. A genetic map was constructed consisting of 1023 single nucleotide polymorphism (SNP) markers clustered into 12 linkage groups and spanning a total of 1,263.87 cM. A reciprocal translocation that differentiates the domesticated genome from its wild ancestor and other related species was identified between chromosomes 1 and 8. Quantitative trait locus (QTL) analysis detected 20 marker-trait associations for 13 phenotypes, from which 14 corresponded to previously identified loci, and six were novel genomic regions related to previously unexplored domestication-syndrome traits, including form of unripe fruit, seedlessness, deciduous fruit, and growth habit. Our results revealed that the genetic architecture of Capsicum domestication is similar to other domesticated species with few loci with large effects, the presence of QTLs clusters in different genomic regions, and the predominance of domesticated recessive alleles. Our analysis indicates the domestication process in chili pepper has also had an effect on traits not directly related to the domestication syndrome. The information obtained in this study provides a more complete understanding of the genetic basis of Capsicum domestication that can potentially guide strategies for the exploitation of wild alleles.
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Affiliation(s)
- Hector Lopez-Moreno
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Ana Celia Basurto-Garduño
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | | | - Eric Diaz-Valenzuela
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Sergio Arellano-Arciniega
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
| | - Juan Zalapa
- Department of Horticulture, University of WI-Madison, Madison, WI, United States
- USDA-ARS Vegetable Crops Research Unit, Department of Horticulture University of WI-Madison, Madison, WI, United States
| | - Ruairidh J. H. Sawers
- Department of Plant Science, The Pennsylvania State University, State College, PA, United States
| | - Angelica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genomica Avanzada (Langebio), Irapuato, Mexico
| | - Luis Diaz-Garcia
- Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias Campo Experimental AGS, Pabellón de Arteaga, Mexico
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Cao Y, Zhang K, Yu H, Chen S, Xu D, Zhao H, Zhang Z, Yang Y, Gu X, Liu X, Wang H, Jing Y, Mei Y, Wang X, Lefebvre V, Zhang W, Jin Y, An D, Wang R, Bosland P, Li X, Paran I, Zhang B, Giuliano G, Wang L, Cheng F. Pepper variome reveals the history and key loci associated with fruit domestication and diversification. MOLECULAR PLANT 2022; 15:1744-1758. [PMID: 36176193 DOI: 10.1016/j.molp.2022.09.021] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum spp.) is an important vegetable crop that provides a unique pungent sensation when eaten. Through construction of a pepper variome map, we examined the main groups that emerged during domestication and breeding of C. annuum, their relationships and temporal succession, and the molecular events underlying the main transitions. The results showed that the initial differentiation in fruit shape and pungency, increase in fruit weight, and transition from erect to pendent fruits, as well as the recent appearance of large, blocky, sweet fruits (bell peppers), were accompanied by strong selection/fixation of key alleles and introgressions in two large genomic regions. Furthermore, we identified Up, which encodes a BIG GRAIN protein involved in auxin transport, as a key domestication gene that controls erect vs pendent fruit orientation. The up mutation gained increased expression especially in the fruit pedicel through a 579-bp sequence deletion in its 5' upstream region, resulting in the phenotype of pendent fruit. The function of Up was confirmed by virus-induced gene silencing. Taken together, these findings constitute a cornerstone for understanding the domestication and differentiation of a key horticultural crop.
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Affiliation(s)
- Yacong Cao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Kang Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hailong Yu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Shumin Chen
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Donghui Xu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Hong Zhao
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Zhenghai Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yinqing Yang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiaozhen Gu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xinyan Liu
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Haiping Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yaxin Jing
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yajie Mei
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Xiang Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Véronique Lefebvre
- INRAE, GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, 84140 Montfavet, France
| | - Weili Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Yuan Jin
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Dongliang An
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Risheng Wang
- Institute of Vegetables, Academy of Agricultural Sciences of Guangxi, 174 Daxue East Road, Nanning 53007, P. R. China
| | - Paul Bosland
- Department of Plant and Environmental Sciences, NMSU, Las Cruces, NM 88003, USA
| | - Xixiang Li
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Ilan Paran
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion, Israel
| | - Baoxi Zhang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China
| | - Giovanni Giuliano
- Biotechnology and Agroindustry Division, ENEA, Italian National Agency for New Technologies, Energy and Sustainable Development, Via Anguillarese, 301-00123 Roma, Italy.
| | - Lihao Wang
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
| | - Feng Cheng
- Key Laboratory of Vegetables, Genetics, and Physiology of China Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture and Rural Affairs, Sino-Dutch Joint Laboratory of Horticultural Genomics, Institute of Vegetables and Flowers, CAAS (Chinese Academy of Agricultural Sciences), 12 Zhongguancun South Street, Beijing 100081, P. R. China.
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9
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Yi S, Lee DG, Back S, Hong JP, Jang S, Han K, Kang BC. Genetic mapping revealed that the Pun2 gene in Capsicum chacoense encodes a putative aminotransferase. FRONTIERS IN PLANT SCIENCE 2022; 13:1039393. [PMID: 36388488 PMCID: PMC9664168 DOI: 10.3389/fpls.2022.1039393] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Several genes regulating capsaicinoid biosynthesis including Pun1 (also known as CS), Pun3, pAMT, and CaKR1 have been studied. However, the gene encoded by Pun2 in the non-pungent Capsicum chacoense is unknown. This study aimed to identify the Pun2 gene by genetic mapping using interspecific (C. chacoense × Capsicum annuum) and intraspecific (C. chacoense × C. chacoense) populations. QTL mapping using the interspecific F2 population revealed two major QTLs on chromosomes 3 and 9. Two bin markers within the QTL regions on two chromosomes were highly correlated with the capsaicinoid content in the interspecific population. The major QTL, Pun2_PJ_Gibbs_3.11 on chromosome 3, contained the pAMT gene, indicating that the non-pungency of C. chacoense may be attributed to a mutation in the pAMT gene. Sequence analysis revealed a 7 bp nucleotide insertion in the 8th exon of pAMT of the non-pungent C. chacoense. This mutation resulted in the generation of an early stop codon, resulting in a truncated mutant lacking the PLP binding site, which is critical for pAMT enzymatic activity. This insertion co-segregated with the pungency phenotype in the intraspecific F2 population. We named this novel pAMT allele pamt11 . Taken together, these data indicate that the non-pungency of C. chacoense is due to the non-functional pAMT allele, and Pun2 encodes the pAMT gene.
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10
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Wang Q, Liao Z, Zhu C, Gou X, Liu Y, Xie W, Wu F, Feng X, Xu J, Li J, Lu Y. Teosinte confers specific alleles and yield potential to maize improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3545-3562. [PMID: 36121453 DOI: 10.1007/s00122-022-04199-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
Teosinte improves maize grain yield and broadens the maize germplasm. Seventy-one quantitative trait loci associated with 24 differential traits between maize and teosinte were identified. Maize is a major cereal crop with a narrow germplasm that has limited its production and breeding progress. Teosinte, an ancestor of maize, provides valuable genetic resources for maize breeding. To identify the favorable alien alleles in teosinte and its yield potential for maize breeding, 4 backcrossed maize-teosinte recombinant inbred line (RIL) populations were cultivated under five conditions. A North Carolina mating design II experiment was conducted on inbred lines with B73 and Mo17 pedigree backgrounds to analyze their combining ability. Abundant phenotypic variation on 26 traits of four RIL populations were found, of which barren tip length, kernel height, and test weight showed positive genetic improvement potential. The hybrid FM132 (BD138/MP116) showed a superior grain yield to that of the check, with an average yield gain of 4.86%. Moreover, inbred lines BD138 and MP048 showed a higher general grain yield combining ability than those of their corresponding checks. We screened 4,964,439 high-quality single-nucleotide polymorphisms in the BD (B73/Zea diploperennis) RIL population for bin construction and used 2322 bin markers for genetic map construction and quantitative trait loci (QTL) mapping. Via inclusive composite interval mapping, 71 QTL associated with 24 differential traits were identified. Gene annotation and transcriptional expression suggested that Zm00001eb352570 and Zm00001eb352580, both annotated as ethylene-responsive transcription factors, were key candidate genes that regulate ear height and the ratio of ear to plant height. Our results indicate that teosinte could broaden the narrow maize germplasm, improve yield potential, and provide desirable alleles for maize breeding.
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Affiliation(s)
- Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Zhengqiao Liao
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
- College of Life Science and Technology, Mianyang Teachers' College, Mianyang, China
| | - Chuntao Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Xiangjian Gou
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Wubing Xie
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Jingwei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang District, China.
- Maize Research Institute, Sichuan Agricultural University, Wenjiang District, China.
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11
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Lee JH, Venkatesh J, Jo J, Jang S, Kim GW, Kim JM, Han K, Ro N, Lee HY, Kwon JK, Kim YM, Lee TH, Choi D, Van Deynze A, Hill T, Kfir N, Freiman A, Davila Olivas NH, Elkind Y, Paran I, Kang BC. High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers. HORTICULTURE RESEARCH 2022; 9:uhac210. [PMID: 36467270 PMCID: PMC9715575 DOI: 10.1093/hr/uhac210] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar 'Dempsey' and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.
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Affiliation(s)
| | | | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Siyoung Jang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Min Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Doil Choi
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Nir Kfir
- NRGene, 5 Golda Meir St., Ness Ziona 7403649, Israel
| | - Aviad Freiman
- Top Seeds International Ltd. Moshav Sharona, 1523200, Israel
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12
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Guan W, Ke C, Tang W, Jiang J, Xia J, Xie X, Yang M, Duan C, Wu W, Zheng Y. Construction of a High-Density Recombination Bin-Based Genetic Map Facilitates High-Resolution Mapping of a Major QTL Underlying Anthocyanin Pigmentation in Eggplant. Int J Mol Sci 2022; 23:ijms231810258. [PMID: 36142175 PMCID: PMC9499331 DOI: 10.3390/ijms231810258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 02/08/2023] Open
Abstract
High-density genetic maps can significantly improve the resolution of QTL mapping. We constructed a high-density recombination bin-based genetic map of eggplant based on 200 F2 plants from an interspecific cross (Solanum melongena × S. incanum) using the whole genome resequencing strategy. The map was 2022.8 cM long, covering near 99% of the eggplant genome. The map contained 3776 bins, with 3644 (96.5%) being effective (position non-redundant) ones, giving a nominal average distance of 0.54 cM and an effective average distance of 0.56 cM between adjacent bins, respectively. Using this map and 172 F2:3 lines, a major QTL with pleiotropic effects on two anthocyanin pigmentation-related traits, leaf vein color (LVC) and fruit pericarp color (FPC), was steadily detected in a bin interval of 2.28 cM (or 1.68 Mb) on chromosome E10 in two cropping seasons, explaining ~65% and 55% of the phenotypic variation in LVC and FPC, respectively. Genome-wide association analysis in this population validated the QTL and demonstrated the correctness of mapping two bins of chromosome E02 onto E10. Bioinformatics analysis suggested that a WDR protein gene inside the bin interval with reliable effective variation between the two parents could be a possible candidate gene of the QTL.
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Affiliation(s)
- Wenxiang Guan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Changjiao Ke
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiqi Tang
- Marine and Agricultural Biotechnology Laboratory, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou 350108, China
| | - Jialong Jiang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jing Xia
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaofang Xie
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mei Yang
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chenfeng Duan
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Weiren Wu
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
| | - Yan Zheng
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, College of Agriculture/College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (W.W.); (Y.Z.)
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13
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Kim Y, Kim GW, Han K, Lee HY, Jo J, Kwon JK, Lemmon Z, Lippman Z, Kang BC. Identification of Genetic Factors Controlling the Formation of Multiple Flowers Per Node in Pepper ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2022; 13:884338. [PMID: 35615119 PMCID: PMC9125326 DOI: 10.3389/fpls.2022.884338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Flower production provides the foundation for crop yield and increased profits. Capsicum annuum is a pepper species with a sympodial shoot structure with solitary flowers. By contrast, C. chinense produces multiple flowers per node. C. annuum accounts for 80% of pepper production worldwide. The identification of C. chinense genes that control multiple flowers and their transfer into C. annuum may open the way to increasing fruit yield. In this study, we dissected the genetic factors were dissected controlling the multiple-flower-per-node trait in Capsicum. 85 recombinant inbred lines (RILs) between the contrasting C. annuum 'TF68' and C. chinense 'Habanero' accessions were phenotyped and genotyped. Quantitative Trait Loci (QTL) analysis identified four novel QTLs on chromosomes 1, 2, 7, and 11 that accounted for 65% of the total phenotypic variation. Genome-wide association study was also performed on a panel of 276 genotyped and phenotyped C. annuum accessions, which revealed 28 regions significantly associated with the multiple-flower trait, of which three overlapped the identified QTLs. Five candidate genes involved in the development of the shoot and flower meristems were identified and these genes could cause multiple flowers per node in pepper. These results contribute to our understanding of multiple flower formation in Capsicum and will be useful to develop high-yielding cultivars.
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Affiliation(s)
- Youngin Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Zachary Lippman
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, New York, NY, United States
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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14
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Kang Y, Lee K, Hoshikawa K, Kang M, Jang S. Molecular Bases of Heat Stress Responses in Vegetable Crops With Focusing on Heat Shock Factors and Heat Shock Proteins. FRONTIERS IN PLANT SCIENCE 2022; 13:837152. [PMID: 35481144 PMCID: PMC9036485 DOI: 10.3389/fpls.2022.837152] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/09/2022] [Indexed: 05/09/2023]
Abstract
The effects of the climate change including an increase in the average global temperatures, and abnormal weather events such as frequent and severe heatwaves are emerging as a worldwide ecological concern due to their impacts on plant vegetation and crop productivity. In this review, the molecular processes of plants in response to heat stress-from the sensing of heat stress, the subsequent molecular cascades associated with the activation of heat shock factors and their primary targets (heat shock proteins), to the cellular responses-have been summarized with an emphasis on the classification and functions of heat shock proteins. Vegetables contain many essential vitamins, minerals, antioxidants, and fibers that provide many critical health benefits to humans. The adverse effects of heat stress on vegetable growth can be alleviated by developing vegetable crops with enhanced thermotolerance with the aid of various genetic tools. To achieve this goal, a solid understanding of the molecular and/or cellular mechanisms underlying various responses of vegetables to high temperature is imperative. Therefore, efforts to identify heat stress-responsive genes including those that code for heat shock factors and heat shock proteins, their functional roles in vegetable crops, and also their application to developing vegetables tolerant to heat stress are discussed.
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Affiliation(s)
- Yeeun Kang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
| | - Kwanuk Lee
- National Institute of Horticultural and Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju-gun, South Korea
| | - Ken Hoshikawa
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | | | - Seonghoe Jang
- World Vegetable Center Korea Office, Wanju-gun, South Korea
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15
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Siddique MI, Lee JH, Ahn JH, Kusumawardhani MK, Safitri R, Harpenas A, Kwon JK, Kang BC. Genotyping-by-sequencing-based QTL mapping reveals novel loci for Pepper yellow leaf curl virus (PepYLCV) resistance in Capsicum annuum. PLoS One 2022; 17:e0264026. [PMID: 35176091 PMCID: PMC8853517 DOI: 10.1371/journal.pone.0264026] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/01/2022] [Indexed: 11/18/2022] Open
Abstract
Disease caused by Pepper yellow leaf curl virus (PepYLCV) is one of the greatest threats to pepper (Capsicum spp.) cultivation in the tropics and subtropics. Resistance to PepYLCV was previously identified in a few Capsicum accessions, but no resistance QTLs have been mapped. This study aimed to elucidate the genetics of PepYLCV resistance in C. annuum L. Augmented inoculation by the viruliferous whitefly Bemisia tabaci was used to evaluate parental lines and an F2 segregating population derived from a cross between resistant C. annuum line LP97 and susceptible C. annuum line ECW30R. Final evaluation was performed six weeks after inoculation using a standardized 5-point scale (0 = no symptoms to 4 = very severe symptoms). A high-density linkage map was constructed using genotyping-by-sequencing (GBS) to identify single-nucleotide polymorphism (SNP) markers associated with PepYLCV resistance in the F2 population. QTL analysis revealed three QTLs, peplcv-1, peplcv-7, and peplcv-12, on chromosomes P1, P7, and P12, respectively. Candidate genes associated with PepYLCV resistance in the QTL regions were inferred. In addition, single markers Chr7-LCV-7 and Chr12-LCV-12 derived from the QTLs were developed and validated in another F2 population and in commercial varieties. This work thus provides not only information for mapping PepYLCV resistance loci in pepper but also forms the basis for future molecular analysis of genes involved in PepYLCV resistance.
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Affiliation(s)
- Muhammad Irfan Siddique
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Joung-Ho Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | | | | | - Ramadhani Safitri
- Department of Plant Pathology, East West Seed Indonesia, West Java, Indonesia
| | - Asep Harpenas
- Department of Plant Pathology, East West Seed Indonesia, West Java, Indonesia
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea
- * E-mail:
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16
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Identification of Fruit Traits Related QTLs and a Candidate Gene, CaBRX, Controlling Locule Number in Pepper (Capsicum annuum L.). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fruit traits are important in pepper (Capsicum annuum L.) and affect its quality and yield. These traits are controlled by quantitative trait loci (QTLs). In this study, we identified many major QTLs that control fruit length (Ftl), fruit diameter (Ftd), fruit shape (Fts), fruit weight (Ftw) and locule number (Lcn) in the F2 and F2:3 populations developed from the QTL mapping of GS6 (P1) and Qiemen (P2). A total of 111 simple sequence repeats and insertion/deletion markers were utilized to construct a linkage map with 12 linkage groups over a length of 1320.72 cM. An inclusive composite interval mapping analysis indicated that many QTLs were detected and included ftl2.1, ftd2.1, fts1.1, ftw2.1 and lcn1.1. As a novel QTL, lcn1.1 was located between HM1112 and EPMS709, and the genetic distance was 3.18 cM covering 60 predicted genes. Within the region, we identified Capana01g004285 as a candidate gene by functional annotation and expression analysis and found that it encodes the BREVIS RADIX (BRX) protein. Knockdown of CaBRX through the virus-induced gene silencing approach in GS6 reduced the number of locules and influenced the expressions of genes related to flower and locule development, suggesting that CaBRX plays an important function in the development of locules.
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Ou C, Sun T, Liu X, Li C, Li M, Wang X, Ren H, Zhao Z, Zhuang F. Detection of Chromosomal Segments Introgressed from Wild Species of Carrot into Cultivars: Quantitative Trait Loci Mapping for Morphological Features in Backcross Inbred Lines. PLANTS (BASEL, SWITZERLAND) 2022; 11:391. [PMID: 35161370 PMCID: PMC8840429 DOI: 10.3390/plants11030391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
Cultivated carrot is thought to have been domesticated from a wild species, and various phenotypes developed through human domestication and selection over the past several centuries. Little is known about the genomic contribution of wild species to the phenotypes of present-day cultivars, although several studies have focused on identifying genetic loci that contribute to the morphology of storage roots. A backcross inbred line (BIL) population derived from a cross between the wild species Daucus carota ssp. carota "Songzi" and the orange cultivar "Amsterdam forcing" was developed. The morphological features in the BIL population became more diverse after several generations of selfing BC2F1 plants. Only few lines retained features of wild parent. Genomic resequencing of the two parental lines and the BILs resulted in 3,223,651 single nucleotide polymorphisms (SNPs), and 13,445 bin markers were generated using a sliding window approach. We constructed a genetic map with 2027 bins containing 154,776 SNPs; the total genetic distance was 1436.43 cM and the average interval between the bins was 0.71 cm. Five stable QTLs related to root length, root shoulder width, dry material content of root, and ratio of root shoulder width to root middle width were consistently detected on chromosome 2 in both years and explained 23.4-66.9% of the phenotypic variance. The effects of introgressed genomic segments from the wild species on the storage root are reported and will enable the identification of functional genes that control root morphological traits in carrot.
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Affiliation(s)
- Chenggang Ou
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Tingting Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Xing Liu
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Chengjiang Li
- Suzhou Academy of Agricultural Science, Suzhou 234000, China; (C.L.); (H.R.)
| | - Min Li
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Xuewei Wang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Huaifu Ren
- Suzhou Academy of Agricultural Science, Suzhou 234000, China; (C.L.); (H.R.)
| | - Zhiwei Zhao
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
| | - Feiyun Zhuang
- Key Laboratory of Horticultural Crop Biology and Germplasm Innovation, Ministry of Agriculture, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Science, Beijing 100081, China; (C.O.); (T.S.); (X.L.); (M.L.); (X.W.); (Z.Z.)
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Borovsky Y, Raz A, Doron-Faigenboim A, Zemach H, Karavani E, Paran I. Pepper Fruit Elongation Is Controlled by Capsicum annuum Ovate Family Protein 20. FRONTIERS IN PLANT SCIENCE 2022; 12:815589. [PMID: 35058962 PMCID: PMC8763684 DOI: 10.3389/fpls.2021.815589] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/02/2021] [Indexed: 05/28/2023]
Abstract
Fruit shape is one of the most important quality traits of pepper (Capsicum spp.) and is used as a major attribute for the classification of fruit types. Wide natural variation in fruit shape exists among the major cultivated species Capsicum annuum, allowing the identification of several QTLs controlling the trait. However, to date, no genes underlying fruit shape QTLs have been conclusively identified, nor has their function been verified in pepper. We constructed a mapping population from a cross of round- and elongated-fruited C. annuum parents and identified a single major QTL on chromosome 10, termed fs10, explaining 68 and 70% of the phenotypic variation for fruit shape index and for distal fruit end angle, respectively. The QTL was mapped in several generations and was localized to a 5 Mbp region containing the ortholog of SlOFP20 that suppresses fruit elongation in tomato. Virus-induced gene silencing of the pepper ortholog CaOFP20 resulted in increased fruit elongation on two independent backgrounds. Furthermore, CaOFP20 exhibited differential expression in fs10 near-isogenic lines, as well as in an association panel of elongated- and round-fruited accessions. A 42-bp deletion in the upstream region of CaOFP20 was most strongly associated with fruit shape variation within the locus. Histological observations in ovaries and fruit pericarps indicated that fs10 exerts its effect on fruit elongation by controlling cell expansion and replication. Our results indicate that CaOFP20 functions as a suppressor of fruit elongation in C. annuum and is the most likely candidate gene underlying fs10.
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Oh YL, Choi IG, Jang KY, Kim MS, Oh MJ, Im JH. SNP-Based Genetic Linkage Map and Quantitative Trait Locus Mapping Associated with the Agronomically Important Traits of Hypsizygus marmoreus. MYCOBIOLOGY 2021; 49:589-598. [PMID: 35035250 PMCID: PMC8725901 DOI: 10.1080/12298093.2021.2018784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
White strains of Hypsizygus marmoreus are more difficult to cultivate than are brown strains; therefore, new white strain breeding strategies are required. Accordingly, we constructed the genetic map of H. marmoreus with 1996 SNP markers on 11 linkage groups (LGs) spanning 1380.49 cM. Prior to analysis, 82 backcrossed strains (HM8 lines) were generated by mating between KMCC03106-31 and the progenies of the F1 hybrid (Hami-18 × KMCC03106-93). Using HM8, the first 23 quantitative trait loci (QTLs) of yield-related traits were detected with high limit of detection (LOD) scores (1.98-9.86). The length, thickness, and hardness of the stipe were colocated on LG 1. Especially, length of stipe and thickness of stipe were highly correlated given that the correlation coefficients were negative (-0.39, p value ≤ .01). And a typical biomodal distribution was observed for lightness of the pileus and the lightness of the pileus trait belonged to the LG 8, as did traits of earliness and mycelial growth in potato dextrose agar (PDA) medium. Therefore, results for color traits can be suggested that color is controlled by a multi-gene of one locus. The yield trait was highly negatively correlated with the traits for thickness of the stipe (-0.45, p value ≤ .01). Based on additive effects, the white strain was confirmed as recessive; however, traits of mycelial growth, lightness, and quality were inherited by backcrossed HM8 lines. This new genetic map, finely mapped QTLs, and the strong selection markers could be used in molecular breeding of H. marmoreus.
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Affiliation(s)
- Youn-Lee Oh
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Korea
| | - In-Geol Choi
- Department of Biotechnology, College of Life Science and Biotechnology, Korea University, Seoul, Korea
| | - Kab-Yeul Jang
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Min-Seek Kim
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Min ji Oh
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
| | - Ji-Hoon Im
- Mushroom Science Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumseong, Korea
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20
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Hu F, Cheng J, Dong J, Zhong J, Zhou Z, Hu K. Fine mapping and candidate gene analysis of the up locus determining fruit orientation in pepper (Capsicum spp.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2901-2911. [PMID: 34076730 DOI: 10.1007/s00122-021-03867-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
The up locus determining fruit orientation was fine-mapped into a region with a physical length of ~169.51 kb on chromosome P12 in pepper. Capana12g000958, encoding a developmentally regulated G protein 2, was proposed as the strongest candidate via sequence comparison and expression analysis. Fruit orientation is an important horticultural and domesticated trait, which is controlled by a single semi-dominant gene (up) in pepper. However, the gene underlying up locus has not yet been identified. In this study, the previously detected major QTL UP12.1 was firstly verified using a backcross population (n = 225) stem from the cross of BB3 (C. annuum) and its wild relative Chiltepin (C. annuum var. glabriusculum) using BB3 as the recurrent parent. Then, a large BC1F2 population (n = 1827) was used for recombinant screening to delimit the up locus into an interval with ~ 169.51 kb in length. Sequence comparison and expression analysis suggested that Capana12g000958, encoding a developmentally regulated G protein 2, was the most likely candidate gene for the up locus. There is no difference within the coding sequences of Capana12g000958 between BB3 and Chiltepin, while a SNP in the upstream of Capana12g000958 showed a complete correlation with the fruit orientation among a panel of 40 diverse pepper inbred lines. These findings will form a basis for gene isolation and reveal of genetic mechanism underlying the fruit orientation domestication in pepper.
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Affiliation(s)
- Fang Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, China
| | - Jiaowen Cheng
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, China
| | - Jichi Dong
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, China
| | - Jian Zhong
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, China
| | - Ziyan Zhou
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center, Guangzhou, 510642, China.
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21
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Solomon AM, Kim TG, Han K, Lee HY, Patil A, Siddique MI, Ahn J, Kang BC. Fine Mapping and Candidate Gene Identification for the CapUp Locus Controlling Fruit Orientation in Pepper ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:675474. [PMID: 34262581 PMCID: PMC8273576 DOI: 10.3389/fpls.2021.675474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
The orientation of fruits is a distinguishing morphological feature of pepper (Capsicum spp.) varieties. The pendent (downward curved) growth of the fruit stalks, known as pedicels, is highly correlated with fruit weight and pedicel length. A previous genetic analysis revealed that the pendent fruit orientation is governed by a dominant gene, and incomplete inheritance is also observed in some Capsicum accessions. To identify and localize this gene, a single quantitative trait locus (QTL) analysis was performed on one F2 and two recombinant inbred line (RIL) populations, and a genome-wide association study (GWAS) was performed using a core collection. Common QTL regions associated with fruit orientation were detected on chromosome 12. A total of 187,966 SNPs were identified in a genotyping-by-sequencing (GBS) for GWAS analysis of 196 Capsicum annuum, 25 Capsicum baccatum, 21 Capsicum chinense, and 14 Capsicum frutescens accessions, representing the germplasm collection of South Korea. The results of these analyses enabled us to narrow down the CapUp region of interest to 200-250 Mbp on chromosome 12. Seven candidate genes were found to be located between two markers that were completely cosegregated with the fruit orientation phenotype. The findings and markers developed in this study will be helpful for additional understanding of pepper fruit development and breeding for fruit orientation.
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Affiliation(s)
- Abate Mekonnen Solomon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Tae-Gun Kim
- Interdisciplinary Program in Agricultural Genomics, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Koeun Han
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Abhinandan Patil
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Muhammad Irfan Siddique
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | | | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- Interdisciplinary Program in Agricultural Genomics, Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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22
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Lee SY, Jang SJ, Jeong HB, Lee SY, Venkatesh J, Lee JH, Kwon JK, Kang BC. A mutation in Zeaxanthin epoxidase contributes to orange coloration and alters carotenoid contents in pepper fruit (Capsicum annuum). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1692-1707. [PMID: 33825226 DOI: 10.1111/tpj.15264] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/16/2021] [Accepted: 03/31/2021] [Indexed: 05/28/2023]
Abstract
Phytoene synthase (PSY1), capsanthin-capsorubin synthase (CCS), and pseudo-response regulator 2 (PRR2) are three major genes controlling fruit color in pepper (Capsicum spp.). However, the diversity of fruit color in pepper cannot be completely explained by these three genes. Here, we used an F2 population derived from Capsicum annuum 'SNU-mini Orange' (SO) and C. annuum 'SNU-mini Yellow' (SY), both harboring functional PSY1 and mutated CCS, and observed that yellow color was dominant over orange color. We performed genotyping-by-sequencing and mapped the genetic locus to a 6.8-Mb region on chromosome 2, which we named CaOr. We discovered a splicing mutation in the zeaxanthin epoxidase (ZEP) gene within this region leading to a premature stop codon. HPLC analysis showed that SO contained higher amounts of zeaxanthin and total carotenoids in mature fruits than SY. A color complementation assay using Escherichia coli harboring carotenoid biosynthetic genes showed that the mutant ZEP protein had reduced enzymatic activity. Transmission electron microscopy of plastids revealed that the ZEP mutation affected plastid development with more rod-shaped inner membrane structures in chromoplasts of mature SO fruits. To validate the role of ZEP in fruit color formation, we performed virus-induced gene silencing of ZEP in the yellow-fruit cultivar C. annuum 'Micropep Yellow' (MY). The silencing of ZEP caused significant changes in the ratios of zeaxanthin to its downstream products and increased total carotenoid contents. Thus, we conclude that the ZEP genotype can determine orange or yellow mature fruit color in pepper.
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Affiliation(s)
- Seo-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - So-Jeong Jang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Hyo-Bong Jeong
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Se-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jelli Venkatesh
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Joung-Ho Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea
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Zhang L, Gong W, Li C, Shen N, Gui Y, Bian Y, Kwan HS, Cheung MK, Xiao Y. RNA-Seq-based high-resolution linkage map reveals the genetic architecture of fruiting body development in shiitake mushroom, Lentinula edodes. Comput Struct Biotechnol J 2021; 19:1641-1653. [PMID: 33868600 PMCID: PMC8026754 DOI: 10.1016/j.csbj.2021.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/07/2021] [Accepted: 03/12/2021] [Indexed: 01/21/2023] Open
Abstract
We constructed a reference genetic map of Lentinula edodes. We re-assembled a chromosome-level genome of L. edodes. We disclosed three hotspots regions for fruiting body-related traits in shiitake. We scanned candidate genes for fruiting body-related traits.
Fruiting body development (FBD) of mushroom-forming fungi has attracted tremendous interest. However, the genetic and molecular basis of FBD is poorly known. Here, using Lentinula edodes (shiitake) as a model, we deciphered the genetic architecture underlying fruiting body-related traits (FBRTs) by combined genomic, genetic and phenotypic data. Using RNA-Seq of fruiting bodies from 110 dikaryons in a bi-parental mapping population, we constructed an ultra-high-density genetic map of L. edodes (Lemap2.0) with a total length of 810.14 cM, which covered 81.7% of the shiitake genome. A total of 94 scaffolds of the shiitake genome were aligned to Lemap2.0 and re-anchored into nine pseudo-chromosomes. Then via quantitative trait locus (QTL) analysis, we disclosed an outline of the genetic architecture of FBD in shiitake. Twenty-nine QTLs and three main genomic regions associated with FBD of shiitake were identified. Using meta-QTL analysis, seven pleiotropic QTLs for multiple traits were detected, which contributed to the correlations of FBRTs. In the mapped QTLs, the expression of 246 genes were found to significantly correlate with the phenotypic traits. Thirty-three of them were involved in FBD and could represent candidate genes controlling the shape and size of fruiting bodies. Collectively, our findings have advanced our understanding of the genetic regulation of FBD in shiitake and mushroom-forming fungi at large.
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Affiliation(s)
- Lin Zhang
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Wenbing Gong
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha 410205, PR China
| | - Chuang Li
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Nan Shen
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Ying Gui
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
| | - Hoi Shan Kwan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China
| | - Man Kit Cheung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin 999077, Hong Kong, China
| | - Yang Xiao
- Institute of Applied Mycology, Huazhong Agricultural University, 430070 Hubei Province, PR China
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Shi TX, Li RY, Zheng R, Chen QF, Li HY, Huang J, Zhu LW, Liang CG. Mapping QTLs for 1000-grain weight and genes controlling hull type using SNP marker in Tartary buckwheat (Fagopyrum tataricum). BMC Genomics 2021; 22:142. [PMID: 33639857 PMCID: PMC7913328 DOI: 10.1186/s12864-021-07449-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum), an important pseudocereal crop, has high economic value due to its nutritional and medicinal properties. However, dehulling of Tartary buckwheat is difficult owing to its thick and tough hull, which has greatly limited the development of the Tartary buckwheat processing industry. The construction of high-resolution genetic maps serves as a basis for identifying quantitative trait loci (QTLs) and qualitative trait genes for agronomic traits. In this study, a recombinant inbred lines (XJ-RILs) population derived from a cross between the easily dehulled Rice-Tartary type and Tartary buckwheat type was genotyped using restriction site-associated DNA (RAD) sequencing to construct a high-density SNP genetic map. Furthermore, QTLs for 1000-grain weight (TGW) and genes controlling hull type were mapped in multiple environments. RESULTS In total, 4151 bin markers comprising 122,185 SNPs were used to construct the genetic linkage map. The map consisted of 8 linkage groups and covered 1444.15 cM, with an average distance of 0.35 cM between adjacent bin markers. Nine QTLs for TGW were detected and distributed on four loci on chromosome 1 and 4. A major locus detected in all three trials was mapped in 38.2-39.8 cM region on chromosome 1, with an LOD score of 18.1-37.0, and explained for 23.6-47.5% of the phenotypic variation. The genes controlling hull type were mapped to chromosome 1 between marker Block330 and Block331, which was closely followed by the major locus for TGW. The expression levels of the seven candidate genes controlling hull type present in the region between Block330 and Block336 was low during grain development, and no significant difference was observed between the parental lines. Six non-synonymous coding SNPs were found between the two parents in the region. CONCLUSIONS We constructed a high-density SNP genetic map for the first time in Tartary buckwheat. The mapped major loci controlling TGW and hull type will be valuable for gene cloning and revealing the mechanism underlying grain development and easy dehulling, and marker-assisted selection in Tartary buckwheat.
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Affiliation(s)
- Tao-Xiong Shi
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China.
| | - Rui-Yuan Li
- Key Laboratory of Information and Computing Science of Guizhou Province, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Ran Zheng
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Qing-Fu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Hong-You Li
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Juan Huang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Li-Wei Zhu
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Cheng-Gang Liang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
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Lee HE, Manivannan A, Lee SY, Han K, Yeum JG, Jo J, Kim J, Rho IR, Lee YR, Lee ES, Kang BC, Kim DS. Chromosome Level Assembly of Homozygous Inbred Line 'Wongyo 3115' Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry ( Fragaria × ananassa). FRONTIERS IN PLANT SCIENCE 2021; 12:696229. [PMID: 34335662 PMCID: PMC8317996 DOI: 10.3389/fpls.2021.696229] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/08/2021] [Indexed: 05/02/2023]
Abstract
Strawberry is an allo-octoploid crop with high genome heterozygosity and complexity, which hinders the sequencing and the assembly of the genome. However, in the present study, we have generated a chromosome level assembly of octoploid strawberry sourced from a highly homozygous inbred line 'Wongyo 3115', using long- and short-read sequencing technologies. The assembly of 'Wongyo 3115' produced 805.6 Mb of the genome with 323 contigs scaffolded into 208 scaffolds with an N50 of 27.3 Mb after further gap filling. The whole genome annotation resulted in 151,892 genes with a gene density of 188.52 (genes/Mb) and validation of a genome, using BUSCO analysis resulted in 94.10% complete BUSCOs. Firmness is one of the vital traits in strawberry, which facilitate the postharvest shelf-life qualities. The molecular and genetic mechanisms that contribute the firmness in strawberry remain unclear. We have constructed a high-density genetic map based on the 'Wongyo 3115' reference genome to identify loci associated with firmness in the present study. For the quantitative trait locus (QTL) identification, the 'BS F2' populations developed from two inbred lines were genotyped, using an Axiom 35K strawberry chip, and marker positions were analyzed based on the 'Wongyo 3115' genome. Genetic maps were constructed with 1,049 bin markers, spanning the 3,861 cM. Using firmness data of 'BS F2' obtained from 2 consecutive years, five QTLs were identified on chromosomes 3-3, 5-1, 6-1, and 6-4. Furthermore, we predicted the candidate genes associated with firmness in strawberries by utilizing transcriptome data and QTL information. Overall, we present the chromosome-level assembly and annotation of a homozygous octoploid strawberry inbred line and a linkage map constructed to identify QTLs associated with fruit firmness.
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Affiliation(s)
- Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Sun Yi Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Jun-Geol Yeum
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jinhee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Il Rae Rho
- Department of Agronomy, Institute of Agriculture and Life Sciences, Gyeongsang National University, Jinju, South Korea
| | - Ye-Rin Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Eun Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju, South Korea
- Do-Sun Kim
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Ayaad M, Han Z, Zheng K, Hu G, Abo-Yousef M, Sobeih SES, Xing Y. Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice. J Adv Res 2020; 28:183-194. [PMID: 33364055 PMCID: PMC7753235 DOI: 10.1016/j.jare.2020.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 07/19/2020] [Accepted: 08/02/2020] [Indexed: 12/18/2022] Open
Abstract
4-way Multiparental population covered the limitations of the biparental structure. The combination of SNP and bin-GWAS showed a powerful tool for QTL mapping. qPGWC8.2 harbored a novel predicted gene for rice chalkiness quality.
Introduction The multiparental population provides us the chance to identify superior alleles controlling a trait for genetic improvement. Genome wide association studies at bin level (bin-GWAS) are expected to be more power in QTL mapping than GWAS at SNP level (SNP-GWAS). Objectives This study is to estimate genetic effects of QTL conferring grain appearance quality in rice by SNP-GWAS and bin-GWAS, compare their power in QTL mapping and identify the superior alleles of all detected QTL from 4 parents for genetic improvement. Methods A 4-way MAGIC population and its four founders were cultivated in two environments to dissect the genetic basis of rice grain appearance quality. Both SNP-GWAS and bin-GWAS were conducted for QTL mapping. Multiple comparison among 4 parental bin/alleles was used to identify the superior alleles. Results A total of 16 and 20 QTL associated with grain appearance quality were identified by SNP- and bin-GWAS, respectively. A minor chalkiness QTL qPGWC8.2/qDEC8 was assigned to a 30-kb genomic region, in which OsMH_08T0121900 is the potential candidate gene because its encoded protein, glucan endo-1,3-beta-glucosidase precursor is involved in the starch and sucrose metabolism pathway. The superior parental alleles for GS3, GL3.1, GW5, GW7, and Chalk5 and two QTLs were almost carried by the high-quality parents Cypress and Yuejingsimiao (YJSM), while the poor-quality parent Guichao-2 (GC2) always carried the inferior alleles. The top five recombinant inbred lines with the highest quality of grain shape and chalkiness traits all carried gene combinations of superior alleles. Conclusions Both SNP- and bin-GWAS methods are encouraged for joint QTL mapping with MAGIC population. qPGWC8.2/qDEC8 is a novel candidate gene strongly associated with chalkiness. The superior alleles of GS3, GW5, GL3.1, GW7, Chalk5 and qPGWC8.2 were identified, and the pyramiding of these superior alleles is helpful to improve rice appearance quality.
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Affiliation(s)
- Mohammed Ayaad
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China.,Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal 13759, Egypt
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Kou Zheng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Gang Hu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
| | - Mahmoud Abo-Yousef
- Rice Research and Training Center, Agriculture Research Center, Sakha 33717, Egypt
| | - Sobeih El S Sobeih
- Plant Research Department, Nuclear Research Center, Atomic Energy Authority, Abo-Zaabal 13759, Egypt
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agriculture University, Wuhan 430070, China
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Zhu D, Li X, Wang Z, You C, Nie X, Sun J, Zhang X, Zhang D, Lin Z. Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton. BMC Genomics 2020; 21:431. [PMID: 32586283 PMCID: PMC7318736 DOI: 10.1186/s12864-020-06800-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 01/07/2023] Open
Abstract
Background The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. Results In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). Conclusions This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.
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Affiliation(s)
- De Zhu
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ximei Li
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Key Laboratory of Dryland Farming Technology/Shandong Engineering Research Center of Germplasm Innovation and Utilization of Salt-tolerant Crops, College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, Shandong, China
| | - Zhiwei Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.,Shandong Peanut Research Institute, Qingdao, 266109, Shangdong, China
| | - Chunyuan You
- Cotton Research Institute, Shihezi Academy of Agriculture Science, Shihezi, Xinjiang, 832003, China
| | - Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Jie Sun
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang Bingtuan, Agricultural College, Shihezi University, Shihezi, Xinjiang, 832003, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dawei Zhang
- Institute of Industrial Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, 830091, China.
| | - Zhongxu Lin
- National Key Laboratory of Crop Genetic Improvement, College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value. Sci Rep 2020; 10:9189. [PMID: 32514106 PMCID: PMC7280500 DOI: 10.1038/s41598-020-66053-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 05/07/2020] [Indexed: 11/08/2022] Open
Abstract
Sweet pepper (Capsicum annuum L.) is a high value crop and one of the most widely grown vegetables belonging to the Solanaceae family. In addition to commercial varieties and F1 hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection. High genetic diversity exists in the landrace gene pool which however has scarcely been studied, thus bounding their cultivation. We re-sequenced four pepper inbred lines, within as many Italian landraces, which representative of as many fruit types: big sized blocky with sunken apex ('Quadrato') and protruding apex or heart shaped ('Cuneo'), elongated ('Corno') and smaller sized sub-spherical ('Tumaticot'). Each genomic sequence was obtained through Illumina platform at coverage ranging from 39 to 44×, and reconstructed at a chromosome scale. About 35.5k genes were predicted in each inbred line, of which 22,017 were shared among them and the reference genome (accession 'CM334'). Distinctive variations in miRNAs, resistance gene analogues (RGAs) and susceptibility genes (S-genes) were detected. A detailed survey of the SNP/Indels occurring in genes affecting fruit size, shape and quality identified the highest frequencies of variation in regulatory regions. Many structural variations were identified as presence/absence variations (PAVs), notably in resistance gene analogues (RGAs) and in the capsanthin/capsorubin synthase (CCS) gene. The large allelic diversity observed in the four inbred lines suggests their potential use as a pre-breeding resource and represents a one-stop resource for C. annuum genomics and a key tool for dissecting the path from sequence variation to phenotype.
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Gong W, Wang Y, Xie C, Zhou Y, Zhu Z, Peng Y. Whole genome sequence of an edible and medicinal mushroom, Hericium erinaceus (Basidiomycota, Fungi). Genomics 2020; 112:2393-2399. [DOI: 10.1016/j.ygeno.2020.01.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/31/2019] [Accepted: 01/20/2020] [Indexed: 02/06/2023]
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Feldmann MJ, Hardigan MA, Famula RA, López CM, Tabb A, Cole GS, Knapp SJ. Multi-dimensional machine learning approaches for fruit shape phenotyping in strawberry. Gigascience 2020; 9:giaa030. [PMID: 32352533 PMCID: PMC7191992 DOI: 10.1093/gigascience/giaa030] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 02/06/2020] [Accepted: 03/10/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Shape is a critical element of the visual appeal of strawberry fruit and is influenced by both genetic and non-genetic determinants. Current fruit phenotyping approaches for external characteristics in strawberry often rely on the human eye to make categorical assessments. However, fruit shape is an inherently multi-dimensional, continuously variable trait and not adequately described by a single categorical or quantitative feature. Morphometric approaches enable the study of complex, multi-dimensional forms but are often abstract and difficult to interpret. In this study, we developed a mathematical approach for transforming fruit shape classifications from digital images onto an ordinal scale called the Principal Progression of k Clusters (PPKC). We use these human-recognizable shape categories to select quantitative features extracted from multiple morphometric analyses that are best fit for genetic dissection and analysis. RESULTS We transformed images of strawberry fruit into human-recognizable categories using unsupervised machine learning, discovered 4 principal shape categories, and inferred progression using PPKC. We extracted 68 quantitative features from digital images of strawberries using a suite of morphometric analyses and multivariate statistical approaches. These analyses defined informative feature sets that effectively captured quantitative differences between shape classes. Classification accuracy ranged from 68% to 99% for the newly created phenotypic variables for describing a shape. CONCLUSIONS Our results demonstrated that strawberry fruit shapes could be robustly quantified, accurately classified, and empirically ordered using image analyses, machine learning, and PPKC. We generated a dictionary of quantitative traits for studying and predicting shape classes and identifying genetic factors underlying phenotypic variability for fruit shape in strawberry. The methods and approaches that we applied in strawberry should apply to other fruits, vegetables, and specialty crops.
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Affiliation(s)
- Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Randi A Famula
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Cindy M López
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Amy Tabb
- USDA-ARS-AFRS, 2217 Wiltshire Rd, Kearneysville, WV 25430, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA
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Cheng J, Chen Y, Hu Y, Zhou Z, Hu F, Dong J, Chen W, Cui J, Wu Z, Hu K. Fine mapping of restorer-of-fertility gene based on high-density genetic mapping and collinearity analysis in pepper (Capsicum annuum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:889-902. [PMID: 31863157 DOI: 10.1007/s00122-019-03513-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/13/2019] [Indexed: 05/24/2023]
Abstract
The pepper restorer-of-fertility (CaRf) gene was fine mapped based on conjoint analysis of recombinants and collinearity between the two pepper reference genomes. Capana06g003028, encoding an Rf-like PPR protein, was proposed as the strongest candidate for pepper CaRf based on sequence comparison and expression analysis. The cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) system not only provides an excellent model to dissect genetic interactions between the mitochondria and nucleus but also plays a vital role in high-efficiency hybrid seed production in crops including pepper (Capsicum spp.). Although two important CMS candidate genes, orf507 and Ψatp6-2, have previously been suggested, the pepper Rf gene (CaRf) has not yet been isolated. In this study, a high-density genetic map comprising 7566 SNP markers in 1944 bins was first constructed with the array genotyping results from 317 F2 individuals. Based on this map, the CaRf gene was preliminarily mapped to a region of 1.15 Mb in length at the end of chromosome P6. Then, by means of a conjoint analysis of recombinants and collinearity between the two pepper reference genomes, an important candidate interval with 270.10 kb in length was delimited for CaRf. Finally, Capana06g003028, which encodes an Rf-like PPR protein, was proposed as the strongest candidate for CaRf based on sequence analysis and expression characteristics in sterile and fertile plants. The high-density genetic map and fine mapping results provided here lay a foundation for the application of molecular breeding, as well as cloning and functional analysis of CaRf, in pepper.
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Affiliation(s)
- Jiaowen Cheng
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Yijian Chen
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Yafei Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Ziyan Zhou
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Fang Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Jichi Dong
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Weili Chen
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China
| | - Junjie Cui
- Department of Horticulture, College of Food Science and Engineering, Foshan University, Foshan, 528200, Guangdong, China
| | - Zhiming Wu
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Kailin Hu
- College of Horticulture, South China Agricultural University/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), Ministry of Agriculture and Rural Affairs/Guangdong Vegetables Engineering Research Center/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables, Guangzhou, 510642, China.
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Jiang S, Yang C, Xu Q, Wang L, Yang X, Song X, Wang J, Zhang X, Li B, Li H, Li Z, Li W. Genetic Dissection of Germinability under Low Temperature by Building a Resequencing Linkage Map in japonica Rice. Int J Mol Sci 2020; 21:ijms21041284. [PMID: 32074988 PMCID: PMC7072905 DOI: 10.3390/ijms21041284] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 02/06/2020] [Accepted: 02/13/2020] [Indexed: 12/17/2022] Open
Abstract
Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties.
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Affiliation(s)
- Shukun Jiang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
- Correspondence: (S.J.); (Z.L.); (W.L.)
| | - Chao Yang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (C.Y.); (X.S.)
| | - Quan Xu
- Rice Research Institute of Shenyang Agricultural University, Shenyang 110866, China; (Q.X.); (J.W.)
| | - Lizhi Wang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Xianli Yang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Xianwei Song
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; (C.Y.); (X.S.)
| | - Jiayu Wang
- Rice Research Institute of Shenyang Agricultural University, Shenyang 110866, China; (Q.X.); (J.W.)
| | - Xijuan Zhang
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Bo Li
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
| | - Hongyu Li
- College of Agronomy, Heilongjiang Bayi Agricultural University, Daqing 163000, China;
| | - Zhugang Li
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
- Correspondence: (S.J.); (Z.L.); (W.L.)
| | - Wenhua Li
- Crop Cultivation and Tillage Institute of Heilongjiang Academy of Agricultural Sciences, Heilongjiang Provincial Key Laboratory of Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China; (L.W.); (X.Y.); (X.Z.); (B.L.)
- Correspondence: (S.J.); (Z.L.); (W.L.)
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Gong W, Xie C, Zhou Y, Zhu Z, Wang Y, Peng Y. A Resequencing-Based Ultradense Genetic Map of Hericium erinaceus for Anchoring Genome Sequences and Identifying Genetic Loci Associated With Monokaryon Growth. Front Microbiol 2020; 10:3129. [PMID: 32082271 PMCID: PMC7005679 DOI: 10.3389/fmicb.2019.03129] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 12/24/2019] [Indexed: 11/25/2022] Open
Abstract
Hericium erinaceus has attracted tremendous interest owing to its compelling health-promoting properties. However, breeding of elite cultivars of H. erinaceus is hindered by the lack of a genetic and molecular toolbox. Here, we performed resequencing analysis of 127 F1 single-spore isolates and constructed the first high-resolution genetic map of H. erinaceus. With the use of recombination bins as markers, an ultradense genetic map consisting of 1,174 bins (including 37,082 single-nucleotide polymorphisms) was generated. This newly developed genetic map covered 1,096.5 cM, with an average bin spacing of 0.95 cM. High collinearity between genetic map and H. erinaceus genome assembly was revealed by aligning scaffolds to this genetic map using bin markers as anchors. The application of this newly developed genetic map in quantitative trait locus (QTL) mapping was also elucidated, and four QTLs for monokaryon growth were recovered. One QTL, mgr1, which contributes 12.1% of growth variations, was located near the mating type A (MAT-A) loci. Overall, this newly constructed high-resolution genetic map (or bin map) could be used as reference in future genetic, genomic, and breeding studies on H. erinaceus.
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Affiliation(s)
| | | | | | | | | | - Yuande Peng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
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Hong JP, Ro N, Lee HY, Kim GW, Kwon JK, Yamamoto E, Kang BC. Genomic Selection for Prediction of Fruit-Related Traits in Pepper ( Capsicum spp.). FRONTIERS IN PLANT SCIENCE 2020; 11:570871. [PMID: 33193503 PMCID: PMC7655793 DOI: 10.3389/fpls.2020.570871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/24/2020] [Indexed: 05/09/2023]
Abstract
Pepper (Capsicum spp.) fruit-related traits are critical determinants of quality. These traits are controlled by quantitatively inherited genes for which marker-assisted selection (MAS) has proven insufficiently effective. Here, we evaluated the potential of genomic selection, in which genotype and phenotype data for a training population are used to predict phenotypes of a test population with only genotype data, for predicting fruit-related traits in pepper. We measured five fruit traits (fruit length, fruit shape, fruit width, fruit weight, and pericarp thickness) in 351 accessions from the pepper core collection, including 229 Capsicum annuum, 48 Capsicum baccatum, 48 Capsicum chinense, 25 Capsicum frutescens, and 1 Capsicum chacoense in 4 years at two different locations and genotyped these accessions using genotyping-by-sequencing. Among the whole core collection, considering its genetic distance and sexual incompatibility, we only included 302 C. annum complex (229 C. annuum, 48 C. chinense, and 25 C. frutescens) into further analysis. We used phenotypic and genotypic data to investigate genomic prediction models, marker density, and effects of population structure. Among 10 genomic prediction methods tested, Reproducing Kernel Hilbert Space (RKHS) produced the highest prediction accuracies (measured as correlation between predicted values and observed values) across the traits, with accuracies of 0.75, 0.73, 0.84, 0.83, and 0.82 for fruit length, fruit shape, fruit width, fruit weight, and pericarp thickness, respectively. Overall, prediction accuracies were positively correlated with the number of markers for fruit traits. We tested our genomic selection models in a separate population of recombinant inbred lines derived from two parental lines from the core collection. Despite the large difference in genetic diversity between the training population and the test population, we obtained moderate prediction accuracies of 0.32, 0.34, 0.50, and 0.48 for fruit length, fruit shape, fruit width, and fruit weight, respectively. This use of genomic selection for fruit-related traits demonstrates the potential use of core collections and genomic selection as tools for crop improvement.
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Affiliation(s)
- Ju-Pyo Hong
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju, South Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Eiji Yamamoto
- Graduate School of Agriculture, Meiji University, Tokyo, Japan
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang,
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Wei J, Li J, Yu J, Cheng Y, Ruan M, Ye Q, Yao Z, Wang R, Zhou G, Deng M, Wan H. Construction of high-density bin map and QTL mapping of horticultural traits from an interspecific cross between Capsicum annuum and Chinese wild Capsicum frutescens. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1787863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Affiliation(s)
- Jiaxiang Wei
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Jun Li
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Jiahong Yu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Yuan Cheng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Meiying Ruan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Qingjing Ye
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Zhuping Yao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Rongqing Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Guozhi Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
| | - Minghua Deng
- College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, Yunnan, PR China
| | - Hongjian Wan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
- China-Australia Research Centre for Crop Improvement, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, PR China
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Lee HY, Ro NY, Patil A, Lee JH, Kwon JK, Kang BC. Uncovering Candidate Genes Controlling Major Fruit-Related Traits in Pepper via Genotype-by-Sequencing Based QTL Mapping and Genome-Wide Association Study. FRONTIERS IN PLANT SCIENCE 2020; 11:1100. [PMID: 32793261 PMCID: PMC7390901 DOI: 10.3389/fpls.2020.01100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/03/2020] [Indexed: 05/09/2023]
Abstract
All modern pepper accessions are products of the domestication of wild Capsicum species. However, due to the limited availability of genome-wide association study (GWAS) data and selection signatures for various traits, domestication-related genes have not been identified in pepper. Here, to address this problem, we obtained data for major fruit-related domestication traits (fruit length, width, weight, pericarp thickness, and fruit position) using a highly diverse panel of 351 pepper accessions representing the worldwide Capsicum germplasm. Using a genotype-by-sequencing (GBS) method, we developed 187,966 genome-wide high-quality SNP markers across 230 C. annuum accessions. Linkage disequilibrium (LD) analysis revealed that the average length of the LD blocks was 149 kb. Using GWAS, we identified 111 genes that were linked to 64 significant LD blocks. We cross-validated the GWAS results using 17 fruit-related QTLs and identified 16 causal genes thought to be associated with fruit morphology-related domestication traits, with molecular functions such as cell division and expansion. The significant LD blocks and candidate genes identified in this study provide unique molecular footprints for deciphering the domestication history of Capsicum. Further functional validation of these candidate genes should accelerate the cloning of genes for major fruit-related traits in pepper.
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Affiliation(s)
- Hea-Young Lee
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Na-Young Ro
- National Academy of Agricultural Science, National Agrobiodiversity Center, Rural Development Administration, Jeonju, South Korea
| | - Abhinandan Patil
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
- *Correspondence: Byoung-Cheorl Kang,
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Zhao S, Zhang C, Mu J, Zhang H, Yao W, Ding X, Ding J, Chang Y. All-in-one sequencing: an improved library preparation method for cost-effective and high-throughput next-generation sequencing. PLANT METHODS 2020; 16:74. [PMID: 32489396 PMCID: PMC7247233 DOI: 10.1186/s13007-020-00615-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 05/14/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Next generation sequencing (NGS) has been widely used in biological research, due to its rapid decrease in cost and increasing ability to generate data. However, while the sequence generation step has seen many improvements over time, the library preparation step has not, resulting in low-efficiency library preparation methods, especially for the most time-consuming and labor-intensive steps: size-selection and quantification. Consequently, there can be bottlenecks in projects with large sample cohorts. RESULTS We have described the all-in-one sequencing (AIO-seq) method, where instead of performing size-selection and quantification for samples individually, one sample one tube, up to 116 samples are pooled and analyzed in a single tube, 'All-In-One'. The AIO-seq method pools libraries based on the samples' expected data yields and the calculated concentrations of the size selected regions (target region), which can easily be obtained with the Agilent 2100 Bioanalyzer and Qubit Fluorometer. AIO-seq was applied to whole genome sequencing and RNA-seq libraries successfully, and it is envisaged that it could be applied to any type of NGS library, such as chromatin immunoprecipitation coupled with massively parallel sequencing, assays for transposase-accessible chromatin with high-throughput sequencing, and high-throughput chromosome conformation capture. We also demonstrated that for genetic population samples with low coverage sequences, like recombinant inbred lines (RIL), AIO-seq could be further simplified, by mixing the libraries immediately after PCR, without calculating the target region concentrations. CONCLUSIONS The AIO-seq method is thus labor saving and cost effective, and suitable for projects with large sample cohorts, like those used in plant breeding or population genetics research.
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Affiliation(s)
- Sheng Zhao
- 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, 518120 China
| | - Cuicui Zhang
- College of Life Science and Technology, Guangxi University, Nanning, 530004 China
| | - Jianqiang Mu
- 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, 518120 China
| | - Hui 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, 518120 China
| | - Wen Yao
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, 450002 China
| | - Xinhua Ding
- State Key Laboratory of Crop Biology, College of Plant Protection, Shandong Agricultural University, Taian, 271018 China
| | - Junqiang Ding
- National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou, 450002 China
| | - Yuxiao Chang
- 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, 518120 China
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Du H, Yang J, Chen B, Zhang X, Zhang J, Yang K, Geng S, Wen C. Target sequencing reveals genetic diversity, population structure, core-SNP markers, and fruit shape-associated loci in pepper varieties. BMC PLANT BIOLOGY 2019; 19:578. [PMID: 31870303 PMCID: PMC6929450 DOI: 10.1186/s12870-019-2122-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/07/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND The widely cultivated pepper (Capsicum spp.) is one of the most diverse vegetables; however, little research has focused on characterizing the genetic diversity and relatedness of commercial varieties grown in China. In this study, a panel of 92 perfect single-nucleotide polymorphisms (SNPs) was identified using re-sequencing data from 35 different C. annuum lines. Based on this panel, a Target SNP-seq genotyping method was designed, which combined multiplex amplification of perfect SNPs with Illumina sequencing, to detect polymorphisms across 271 commercial pepper varieties. RESULTS The perfect SNPs panel had a high discriminating capacity due to the average value of polymorphism information content, observed heterozygosity, expected heterozygosity, and minor allele frequency, which were 0.31, 0.28, 0.4, and 0.31, respectively. Notably, the studied pepper varieties were morphologically categorized based on fruit shape as blocky-, long horn-, short horn-, and linear-fruited. The long horn-fruited population exhibited the most genetic diversity followed by the short horn-, linear-, and blocky-fruited populations. A set of 35 core SNPs were then used as kompetitive allele-specific PCR (KASPar) markers, another robust genotyping technique for variety identification. Analysis of genetic relatedness using principal component analysis and phylogenetic tree construction indicated that the four fruit shape populations clustered separately with limited overlaps. Based on STRUCTURE clustering, it was possible to divide the varieties into five subpopulations, which correlated with fruit shape. Further, the subpopulations were statistically different according to a randomization test and Fst statistics. Nine loci, located on chromosomes 1, 2, 3, 4, 6, and 12, were identified to be significantly associated with the fruit shape index (p < 0.0001). CONCLUSIONS Target SNP-seq developed in this study appears as an efficient power tool to detect the genetic diversity, population relatedness and molecular breeding in pepper. Moreover, this study demonstrates that the genetic structure of Chinese pepper varieties is significantly influenced by breeding programs focused on fruit shape.
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Affiliation(s)
- Heshan Du
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Bin Chen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Xiaofen Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Jian Zhang
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China
| | - Kun Yang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sansheng Geng
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
| | - Changlong Wen
- Beijing Vegetable Research Center (BVRC), Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China.
- Beijing Key Laboratory of Vegetable Germplasm Improvement, National Engineering Research Center for Vegetables, Beijing, 100097, China.
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A recombination bin-map identified a major QTL for resistance to Tomato Spotted Wilt Virus in peanut (Arachis hypogaea). Sci Rep 2019; 9:18246. [PMID: 31796847 PMCID: PMC6890646 DOI: 10.1038/s41598-019-54747-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/17/2019] [Indexed: 11/16/2022] Open
Abstract
Tomato spotted wilt virus (TSWV) is a devastating disease to peanut growers in the South-eastern region of the United States. Newly released peanut cultivars in recent years are crucial as they have some levels of resistance to TSWV. One mapping population of recombinant inbred line (RIL) used in this study was derived from peanut lines of SunOleic 97R and NC94022. A whole genome re-sequencing approach was used to sequence these two parents and 140 RILs. A recombination bin-based genetic map was constructed, with 5,816 bins and 20 linkage groups covering a total length of 2004 cM. Using this map, we identified three QTLs which were colocalized on chromosome A01. One QTL had the largest effect of 36.51% to the phenotypic variation and encompassed 89.5 Kb genomic region. This genome region had a cluster of genes, which code for chitinases, strictosidine synthase-like, and NBS-LRR proteins. SNPs linked to this QTL were used to develop Kompetitive allele specific PCR (KASP) markers, and the validated KASP markers showed expected segregation of alleles coming from resistant and susceptible parents within the population. Therefore, this bin-map and QTL associated with TSWV resistance made it possible for functional gene mapping, map-based cloning, and marker-assisted breeding. This study identified the highest number of SNP makers and demonstrated recombination bin-based map for QTL identification in peanut. The chitinase gene clusters and NBS-LRR disease resistance genes in this region suggest the possible involvement in peanut resistance to TSWV.
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Genome-Wide Correlation of 36 Agronomic Traits in the 287 Pepper ( Capsicum) Accessions Obtained from the SLAF-seq-Based GWAS. Int J Mol Sci 2019; 20:ijms20225675. [PMID: 31766117 PMCID: PMC6888518 DOI: 10.3390/ijms20225675] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Revised: 10/29/2019] [Accepted: 11/04/2019] [Indexed: 11/16/2022] Open
Abstract
There are many agronomic traits of pepper (Capsicum L.) with abundant phenotypes that can benefit pepper growth. Using specific-locus amplified fragment sequencing (SLAF-seq), a genome-wide association study (GWAS) of 36 agronomic traits was carried out for 287 representative pepper accessions. To ensure the accuracy and reliability of the GWAS results, we analyzed the genetic diversity, distribution of labels (SLAF tags and single nucleotide polymorphisms (SNPs)) and population differentiation and determined the optimal statistical model. In our study, 1487 SNPs were highly significantly associated with 26 agronomic traits, and 2126 candidate genes were detected in the 100-kb region up- and down-stream near these SNPs. Furthermore, 13 major association peaks were identified for 11 key agronomic traits. Then we examined the correlations among the 36 agronomic traits and analyzed SNP distribution and found 37 SNP polymerization regions (total size: 264.69 Mbp) that could be selected areas in pepper breeding. We found that the stronger the correlation between the two traits, the greater the possibility of them being in more than one polymerization region, suggesting that they may be linked or that one pleiotropic gene controls them. These results provide a theoretical foundation for future multi-trait pyramid breeding of pepper. Finally, we found that the GWAS signals were highly consistent with those from the nuclear restorer-of-fertility (Rf) gene for cytoplasmic male sterility (CMS), verifying their reliability. We further identified Capana06g002967 and Capana06g002969 as Rf candidate genes by functional annotation and expression analysis, which provided a reference for the study of cytoplasmic male sterility in Capsicum.
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Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites. Sci Rep 2019; 9:10067. [PMID: 31296904 PMCID: PMC6624249 DOI: 10.1038/s41598-019-46136-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/21/2019] [Indexed: 11/18/2022] Open
Abstract
Capsicum is one of the major vegetable crops grown worldwide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Broad variability of fruits has been driven by breeding programs and has been mainly studied by linkage analysis. We discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known major subdivision of C. annuum separates large and bulky fruits from small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080). Our collection covers all the economically important species of Capsicum widely used in breeding programs and represent the widest and largest study so far in terms of the number of species and number of genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results provide a comprehensive and precise perspective on genomic variability in Capsicum at population-level and suggest that future fine genetic association studies will yield useful results for breeding.
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Siddique MI, Lee HY, Ro NY, Han K, Venkatesh J, Solomon AM, Patil AS, Changkwian A, Kwon JK, Kang BC. Identifying candidate genes for Phytophthora capsici resistance in pepper (Capsicum annuum) via genotyping-by-sequencing-based QTL mapping and genome-wide association study. Sci Rep 2019; 9:9962. [PMID: 31292472 PMCID: PMC6620314 DOI: 10.1038/s41598-019-46342-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 06/24/2019] [Indexed: 01/16/2023] Open
Abstract
Phytophthora capsici (Leon.) is a globally prevalent, devastating oomycete pathogen that causes root rot in pepper (Capsicum annuum). Several studies have identified quantitative trait loci (QTL) underlying resistance to P. capsici root rot (PcRR). However, breeding for pepper cultivars resistant to PcRR remains challenging due to the complexity of PcRR resistance. Here, we combined traditional QTL mapping with GWAS to broaden our understanding of PcRR resistance in pepper. Three major-effect loci (5.1, 5.2, and 5.3) conferring broad-spectrum resistance to three isolates of P. capsici were mapped to pepper chromosome P5. In addition, QTLs with epistatic interactions and minor effects specific to isolate and environment were detected on other chromosomes. GWAS detected 117 significant SNPs across the genome associated with PcRR resistance, including SNPs on chromosomes P5, P7, and P11 that colocalized with the QTLs identified here and in previous studies. Clusters of candidate nucleotide-binding site-leucine-rich repeat (NBS-LRR) and receptor-like kinase (RLK) genes were predicted within the QTL and GWAS regions; such genes often function in disease resistance. These candidate genes lay the foundation for the molecular dissection of PcRR resistance. SNP markers associated with QTLs for PcRR resistance will be useful for marker-assisted breeding and genomic selection in pepper breeding.
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Affiliation(s)
- Muhammad Irfan Siddique
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hea-Young Lee
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Na-Young Ro
- National Academy of Agricultural Science, National Agrobiodiversity Center, Rural Development Administration, Jeonju, 54874, Republic of Korea
| | - Koeun Han
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jelli Venkatesh
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Abate Mekonnen Solomon
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Abhinandan Surgonda Patil
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Amornrat Changkwian
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.
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Genetic diversity and population structure of Ethiopian Capsicum germplasms. PLoS One 2019; 14:e0216886. [PMID: 31112575 PMCID: PMC6528999 DOI: 10.1371/journal.pone.0216886] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/30/2019] [Indexed: 11/19/2022] Open
Abstract
We established a collection of 142 Capsicum genotypes from different geographical areas of Ethiopia with the aim of capturing genetic diversity. Morphological traits and high-resolution melting analysis distinguished one Capsicum baccatum, nine Capsicum frutescens and 132 Capsicum annuum accessions in the collection. Measurement of plant growth parameters revealed variation between germplasms in parameters including plant height, stem thickness, internode length, number of side branches, fruit width, and fruit length. Broad-sense heritability was maximum for fruit weight, followed by length and width of leaves. We used genotyping by sequencing (GBS) to identify single-nucleotide polymorphisms (SNPs) in the panel of 142 Capsicum germplasms and found 2,831,791 genome-wide SNP markers. Among these, we selected 53,284 high-quality SNPs and used them to estimate the level of genetic diversity, population structure, and phylogenetic relationships. From model-based ancestry analysis, the phylogenetic tree and principal-coordinate analysis (PCoA), we identified two distinct genetic populations: one comprising 132 C. annuum accessions and the other comprising the nine C. frutescens accessions. GWAS analysis detected 509 SNP markers that were significantly associated with fruit-, stem- and leaf-related traits. This is the first comprehensive report of the analysis of genetic variation in Ethiopian Capsicum species involving a large number of accessions. The results will help breeders utilize the germplasm collection to improve existing commercial cultivars.
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Zhang XF, Wang GY, Dong TT, Chen B, Du HS, Li CB, Zhang FL, Zhang HY, Xu Y, Wang Q, Geng SS. High-density genetic map construction and QTL mapping of first flower node in pepper (Capsicum annuum L.). BMC PLANT BIOLOGY 2019; 19:167. [PMID: 31035914 PMCID: PMC6489210 DOI: 10.1186/s12870-019-1753-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/31/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND First flower node (FFN) is an important trait for evaluating fruit earliness in pepper (Capsicum annuum L.). The trait is controlled by quantitative trait loci (QTL); however, studies have been limited on QTL mapping and genes contributing to the trait. RESULTS In this study, we developed a high density genetic map using specific-locus amplified fragment sequencing (SLAF-seq), a high-throughput strategy for de novo single nucleotide polymorphism discovery, based on 146 recombinant inbred lines (RILs) derived from an intraspecific cross between PM702 and FS871. The map contained 9328 SLAF markers on 12 linkage groups (LGs), and spanned a total genetic distance of 2009.69 centimorgan (cM) with an average distance of 0.22 cM. The sequencing depth for the map was 72.39-fold in the male parent, 57.04-fold in the female parent, and 15.65-fold in offspring. Using the genetic map, two major QTLs, named Ffn2.1 and Ffn2.2, identified on LG02 were strongly associated with FFN, with a phenotypic variance explanation of 28.62 and 19.56%, respectively. On the basis of the current annotation of C. annuum cv. Criollo de Morelos (CM334), 59 candidate genes were found within the Ffn2.1 and Ffn2.2 region, but only 3 of 59 genes were differentially expressed according to the RNA-seq results. Eventually we identified one gene associated with the FFN based on the function through GO, KEGG, and Swiss-prot analysis. CONCLUSIONS Our research showed that the construction of high-density genetic map using SLAF-seq is a valuable tool for fine QTL mapping. The map we constructed is by far the most saturated complete genetic map of pepper, and using it we conducted fine QTL mapping for the important trait, FFN. QTLs and candidate genes obtained in this study lay a good foundation for the further research on FFN-related genes and other genetic applications in pepper.
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Affiliation(s)
- Xiao-fen Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - Guo-yun Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Ting-ting Dong
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Bin Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - He-shan Du
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Chang-bao Li
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Feng-lan Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Hai-ying Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Yong Xu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
| | - Qian Wang
- College of Horticulture, China Agricultural University, Beijing, 100097 People’s Republic of China
| | - San-sheng Geng
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097 People’s Republic of China
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Han K, Jang S, Lee JH, Lee DG, Kwon JK, Kang BC. A MYB transcription factor is a candidate to control pungency in Capsicum annuum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1235-1246. [PMID: 30607439 DOI: 10.1007/s00122-018-03275-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 12/22/2018] [Indexed: 05/13/2023]
Abstract
Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F2 plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.
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Affiliation(s)
- Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Siyoung Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Do-Gyeong Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Vegetable Breeding Research Center, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Gonda I, Ashrafi H, Lyon DA, Strickler SR, Hulse-Kemp AM, Ma Q, Sun H, Stoffel K, Powell AF, Futrell S, Thannhauser TW, Fei Z, Van Deynze AE, Mueller LA, Giovannoni JJ, Foolad MR. Sequencing-Based Bin Map Construction of a Tomato Mapping Population, Facilitating High-Resolution Quantitative Trait Loci Detection. THE PLANT GENOME 2019; 12:180010. [PMID: 30951101 DOI: 10.3835/plantgenome2018.02.0010] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Genotyping-by-sequencing (GBS) was employed to construct a highly saturated genetic linkage map of a tomato ( L.) recombinant inbred line (RIL) population, derived from a cross between cultivar NC EBR-1 and the wild tomato L. accession LA2093. A pipeline was developed to convert single nucleotide polymorphism (SNP) data into genomic bins, which could be used for fine mapping of quantitative trait loci (QTL) and identification of candidate genes. The pipeline, implemented in a python script named SNPbinner, adopts a hidden Markov model approach for calculation of recombination breakpoints followed by genomic bins construction. The total length of the newly developed high-resolution genetic map was 1.2-fold larger than previously estimated based on restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR)-based markers. The map was used to verify and refine QTL previously identified for two fruit quality traits in the RIL population, fruit weight (FW) and fruit lycopene content (LYC). Two well-described FW QTL ( and ) were localized precisely at their known underlying causative genes, and the QTL intervals were decreased by two- to tenfold. A major QTL for LYC content () was verified at high resolution and its underlying causative gene was determined to be ζ (). The RIL population, the high resolution genetic map, and the easy-to-use genotyping pipeline, SNPbinner, are made publicly available.
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Park M, Lee JH, Han K, Jang S, Han J, Lim JH, Jung JW, Kang BC. A major QTL and candidate genes for capsaicinoid biosynthesis in the pericarp of Capsicum chinense revealed using QTL-seq and RNA-seq. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:515-529. [PMID: 30426173 DOI: 10.1007/s00122-018-3238-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/09/2018] [Indexed: 05/09/2023]
Abstract
A major QTL and candidate genes controlling capsaicinoid content in the pericarp were identified by QTL-seq and RNA-seq in Capsicum chinense. Capsaicinoid biosynthesis was previously thought to be restricted to the placental tissue; however, the recent discovery of their biosynthesis in the pericarp provides new opportunities to increase the capsaicinoid content in pepper fruits. Currently, the genetic mechanisms regulating capsaicinoid biosynthesis in the pericarp remain unknown. Here, we performed quantitative trait loci (QTL) mapping and RNA sequencing (RNA-seq) to reveal the genes controlling capsaicinoid biosynthesis in the pericarp. A whole-genome sequencing-based QTL-seq strategy was employed, identifying a major QTL on chromosome 6. To validate the QTL on chromosome 6, we performed traditional QTL mapping using the same population in QTL-seq with an additional biparental population. A total of 15 QTLs for capsaicinoid content distributed on chromosomes 3, 6, and 11 were newly identified. Among these QTLs, the genetic loci on the lower arm of chromosome 6 were commonly detected in the two mapping populations, corresponding to the location of the major QTL detected using whole-genome sequencing-based QTL-seq. Our RNA-seq analysis identified candidate genes within the common QTL that were differentially expressed in the pungent and non-pungent pericarp tissues. Our results are expected to contribute to the elucidation of the regulation of capsaicinoid biosynthesis. We also demonstrated that a combination of QTL mapping and RNA-seq is helpful for refining the candidate genes of a complicated trait of interest.
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Affiliation(s)
- Minjeong Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Joung-Ho Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Koeun Han
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Siyoung Jang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jiwoong Han
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jung-Hyun Lim
- Research Institute of Biotechnology, CJ CheilJedang Corp., Suwon, 16495, Republic of Korea
| | - Ji-Won Jung
- Research Institute of Biotechnology, CJ CheilJedang Corp., Suwon, 16495, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.
- Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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Zhu Z, Sun B, Wei J, Cai W, Huang Z, Chen C, Cao B, Chen G, Lei J. Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits. Sci Rep 2019; 9:1054. [PMID: 30705330 PMCID: PMC6355862 DOI: 10.1038/s41598-018-38370-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 12/27/2018] [Indexed: 11/09/2022] Open
Abstract
The yield of pepper plants (Capsicum spp.) is their most important trait and is affected by the flower number and flowering time. Capsicum annuum produces a single flower per node and has an early flowering habit. By contrast, Capsicum chinense yields multiple flowers per node and has a late flowering character. However, the genetic mechanism underlying the control of these floral traits remains largely unknown. In this study, 150 F2 populations from an interspecific cross between the inbred lines 740 (C. chinense) and CA1 (C. annuum) and their parents were used to construct a molecular genetic linkage map using the specific length amplified fragment sequencing (SLAF-seq) technique. This linkage map, spanning 1,586.78 cM in length, contained 9,038 markers on 12 chromosomes, with a mean marker distance of 0.18 cM. Phenotypic data on the flowering time and flower number per node were collected over multiple years, and QTL analysis identified 6 QTLs for the flowering time and flower number per node by composite interval mapping (CIM) and genome-wide composite interval mapping (GCIM) methods at least in two environments. The candidate genes within the major QTL were predicted. In the major flowering time QTL, the candidate gene Capana02g000700, which encodes the homeotic protein APETALA2, was identified. Quantitative reverse-transcription PCR (qRT-PCR) analysis indicated that its expression level in 740 was higher than that in CA1. Gene expression analysis indicated that the expression of Capana02g000700 was significantly upregulated in flowers, and many floral development-related genes were found to be coexpressed with Capana02g000700, supporting the function of this gene in association with flowering time in C. chinense and C. annuum species.
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Affiliation(s)
- Zhangsheng Zhu
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Binmei Sun
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jianlang Wei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Wen Cai
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Zhubin Huang
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Changming Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bihao Cao
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Guoju Chen
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jianjun Lei
- Key Laboratory of Horticultural Crop Biology and Germplasm innovation in South China, College of Horticulture, South China Agricultural University, Guangzhou, 510642, China.
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Lee J. Development and Evolution of Molecular Markers and Genetic Maps in Capsicum Species. COMPENDIUM OF PLANT GENOMES 2019. [DOI: 10.1007/978-3-319-97217-6_5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Pereira-Dias L, Vilanova S, Fita A, Prohens J, Rodríguez-Burruezo A. Genetic diversity, population structure, and relationships in a collection of pepper ( Capsicum spp.) landraces from the Spanish centre of diversity revealed by genotyping-by-sequencing (GBS). HORTICULTURE RESEARCH 2019; 6:54. [PMID: 31044080 PMCID: PMC6491490 DOI: 10.1038/s41438-019-0132-8] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 01/11/2019] [Accepted: 01/17/2019] [Indexed: 05/03/2023]
Abstract
Pepper (Capsicum spp.) is one of the most important vegetable crops; however, pepper genomic studies lag behind those of other important Solanaceae. Here we present the results of a high-throughput genotyping-by-sequencing (GBS) study of a collection of 190 Capsicum spp. accessions, including 183 of five cultivated species (C. annuum, C. chinense, C. frutescens, C. baccatum, and C. pubescens) and seven of the wild form C. annuum var. glabriusculum. Sequencing generated 6,766,231 high-quality read tags, of which 40.7% were successfully aligned to the reference genome. SNP calling yielded 4083 highly informative segregating SNPs. Genetic diversity and relationships of a subset of 148 accessions, of which a complete passport information was available, was studied using principal components analysis (PCA), discriminant analysis of principal components (DAPC), and phylogeny approaches. C. annuum, C. baccatum, and C. chinense were successfully separated by all methods. Our population was divided into seven clusters by DAPC, where C. frutescens accessions were clustered together with C. chinense. C. annuum var. glabriusculum accessions were spread into two distinct genetic pools, while European accessions were admixed and closely related. Separation of accessions was mainly associated to differences in fruit characteristics and origin. Phylogeny studies showed a close relation between Spanish and Mexican accessions, supporting the hypothesis that the first arose from a main genetic flow from the latter. Tajima's D statistic values were consistent with positive selection in the C. annuum clusters, possibly related to domestication or selection towards traits of interest. This work provides comprehensive and relevant information on the origin and relationships of Spanish landraces and for future association mapping studies in pepper.
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Affiliation(s)
- Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Ana Fita
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
| | - Adrián Rodríguez-Burruezo
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain
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