1
|
Fang X, Zhu Z, Li J, Wang X, Wei C, Zhang X, Dai Z, Liu S, Luan F. Identification of Chromosomal Regions and Candidate Genes for Round leaf Locus in Cucumis melo L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1134. [PMID: 38674543 PMCID: PMC11054961 DOI: 10.3390/plants13081134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024]
Abstract
Leaf morphology plays a crucial role in plant classification and provides a significant model for studying plant diversity while directly impacting photosynthetic efficiency. In the case of melons, leaf shape not only influences production and classification but also represents a key genetic trait that requires further exploration. In this study, we utilized forward genetics to pinpoint a recessive locus, dubbed Cmrl (Round leaf), which is responsible for regulating melon leaf shape. Through bulked segregant analysis sequencing and extensive evaluation of a two-year F2 population, we successfully mapped the Cmrl locus to a 537.07 kb region on chromosome 8 of the melon genome. Subsequent genetic fine-mapping efforts, leveraging a larger F2 population encompassing 1322 plants and incorporating F2:3 phenotypic data, further refined the locus to an 80.27 kb interval housing five candidate genes. Promoter analysis and coding sequence cloning confirmed that one of these candidates, MELO3C019152.2 (Cmppr encoding a pentatricopeptide repeat-containing family protein, Cmppr), stands out as a strong candidate gene for the Cmrl locus. Notably, comparisons of Cmrl expressions across various stages of leaf development and different leaf regions suggest a pivotal role of Cmrl in the morphogenesis of melon leaves.
Collapse
Affiliation(s)
- Xufeng Fang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Zicheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Junyan Li
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xuezheng Wang
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Chunhua Wei
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (C.W.); (X.Z.)
| | - Xian Zhang
- College of Horticulture, Northwest A&F University, Xianyang 712100, China; (C.W.); (X.Z.)
| | - Zuyun Dai
- Anhui Jianghuai Horticulture Technology Co., Ltd., Hefei 230031, China;
| | - Shi Liu
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Feishi Luan
- Key Laboratory of Biology and Genetic Improvement of Horticulture Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China; (X.F.); (Z.Z.); (J.L.); (X.W.)
| |
Collapse
|
2
|
Bernád V, Al-Tamimi N, Langan P, Gillespie G, Dempsey T, Henchy J, Harty M, Ramsay L, Houston K, Macaulay M, Shaw PD, Raubach S, Mcdonnel KP, Russell J, Waugh R, Khodaeiaminjan M, Negrão S. Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT). FRONTIERS IN PLANT SCIENCE 2024; 15:1268847. [PMID: 38571708 PMCID: PMC10987740 DOI: 10.3389/fpls.2024.1268847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 02/28/2024] [Indexed: 04/05/2024]
Abstract
In the last century, breeding programs have traditionally favoured yield-related traits, grown under high-input conditions, resulting in a loss of genetic diversity and an increased susceptibility to stresses in crops. Thus, exploiting understudied genetic resources, that potentially harbour tolerance genes, is vital for sustainable agriculture. Northern European barley germplasm has been relatively understudied despite its key role within the malting industry. The European Heritage Barley collection (ExHIBiT) was assembled to explore the genetic diversity in European barley focusing on Northern European accessions and further address environmental pressures. ExHIBiT consists of 363 spring-barley accessions, focusing on two-row type. The collection consists of landraces (~14%), old cultivars (~18%), elite cultivars (~67%) and accessions with unknown breeding history (~1%), with 70% of the collection from Northern Europe. The population structure of the ExHIBiT collection was subdivided into three main clusters primarily based on the accession's year of release using 26,585 informative SNPs based on 50k iSelect single nucleotide polymorphism (SNP) array data. Power analysis established a representative core collection of 230 genotypically and phenotypically diverse accessions. The effectiveness of this core collection for conducting statistical and association analysis was explored by undertaking genome-wide association studies (GWAS) using 24,876 SNPs for nine phenotypic traits, four of which were associated with SNPs. Genomic regions overlapping with previously characterised flowering genes (HvZTLb) were identified, demonstrating the utility of the ExHIBiT core collection for locating genetic regions that determine important traits. Overall, the ExHIBiT core collection represents the high level of untapped diversity within Northern European barley, providing a powerful resource for researchers and breeders to address future climate scenarios.
Collapse
Affiliation(s)
- Villő Bernád
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Nadia Al-Tamimi
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Patrick Langan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Gary Gillespie
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Timothy Dempsey
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Joey Henchy
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Mary Harty
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Luke Ramsay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kelly Houston
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Malcolm Macaulay
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Paul D. Shaw
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Sebastian Raubach
- Department of Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Kevin P. Mcdonnel
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- School of Biosystems Engineering, University College Dublin, Dublin, Ireland
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
- Division of Plant Sciences, University of Dundee at The James Hutton Institute, Dundee, United Kingdom
| | | | - Sónia Negrão
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| |
Collapse
|
3
|
Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
Collapse
Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| |
Collapse
|
4
|
Yan H, Wang K, Wang M, Feng L, Zhang H, Wei X. QTL Mapping and Genome-Wide Association Study Reveal Genetic Loci and Candidate Genes Related to Soluble Solids Content in Melon. Curr Issues Mol Biol 2023; 45:7110-7129. [PMID: 37754234 PMCID: PMC10530127 DOI: 10.3390/cimb45090450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/28/2023] Open
Abstract
Melon (Cucumis melo L.) is an economically important Cucurbitaceae crop grown around the globe. The sweetness of melon is a significant factor in fruit quality and consumer appeal, and the soluble solids content (SSC) is a key index of melon sweetness. In this study, 146 recombinant inbred lines (RILs) derived from two oriental melon materials with different levels of sweetness containing 1427 bin markers, and 213 melon accessions containing 1,681,775 single nucleotide polymorphism (SNP) markers were used to identify genomic regions influencing SSC. Linkage mapping detected 10 quantitative trait loci (QTLs) distributed on six chromosomes, seven of which were overlapped with the reported QTLs. A total of 211 significant SNPs were identified by genome-wide association study (GWAS), 138 of which overlapped with the reported QTLs. Two new stable, co-localized regions on chromosome 3 were identified by QTL mapping and GWAS across multiple environments, which explained large phenotypic variance. Five candidate genes related to SSC were identified by QTL mapping, GWAS, and qRT-PCR, two of which were involved in hydrolysis of raffinose and sucrose located in the new stable loci. The other three candidate genes were involved in raffinose synthesis, sugar transport, and production of substrate for sugar synthesis. The genomic regions and candidate genes will be helpful for molecular breeding programs and elucidating the mechanisms of sugar accumulation.
Collapse
|
5
|
Liang X, Li Q, Cao L, Du X, Qiang J, Hou J, Li X, Zhu H, Yang S, Liu D, Zhu L, Yang L, Wang P, Hu J. Natural allelic variation in the EamA-like transporter, CmSN, is associated with fruit skin netting in melon. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:192. [PMID: 37603118 DOI: 10.1007/s00122-023-04443-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/08/2023] [Indexed: 08/22/2023]
Abstract
KEY MESSAGE A SNP mutation in CmSN, encoding an EamA-like transporter, is responsible for fruit skin netting in melon. In maturing melon (Cucumis melo L.), the rind becomes reticulated or netted, a unique characteristic that dramatically changes the appearance of the fruit. However, little is known about the molecular basis of fruit skin netting formation in this important cucurbit crop. Here, we conducted map-based cloning of a skin netting (CmSN) locus using segregating populations derived from the cross between the smooth-fruit line H906 and the netted-fruit line H581. The results showed that CmSN was controlled by a single dominant gene and was primarily positioned on melon chromosome 2, within a physical interval of ~ 351 kb. Further fine mapping in a large F2 population narrowed this region to a 71-kb region harboring 5 genes. MELO3C010288, which encodes a protein in the EamA-like transporter family, is the best possible candidate gene for the netted phenotype. Two nonsynonymous single nucleotide polymorphisms (SNPs) were identified in the third and sixth exons of the CmSN gene and co-segregated with the skin netting (SN) phenotype among the genetic population. A genome-wide association study (GWAS) determined that CmSN is probably a domestication gene under selective pressure during the subspecies C. melo subsp. melo differentiation. The SNP in the third exon of CmSN (the leading SNP in GWAS) revealed a bi-allelic diversity in natural accessions with SN traits. Our results lay a foundation for deciphering the molecular mechanism underlying the formation of fruit skin netting in melon, as well as provide a strategy for genetic improvement of netted fruit using a marker-assisted selection approach.
Collapse
Affiliation(s)
- Xiaoxue Liang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Qiong Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Lei Cao
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Xuanyu Du
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Junhao Qiang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
| | - Juan Hou
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Xiang Li
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Huayu Zhu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Sen Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Dongming Liu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Lei Zhu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China
| | - Panqiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China.
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China.
| | - Jianbin Hu
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002, China.
- Henan Engineering Center for Cucurbit Germplasm Enhancement and Utilization, Zhengzhou, 450002, China.
| |
Collapse
|
6
|
Shigita G, Dung TP, Pervin MN, Duong TT, Imoh ON, Monden Y, Nishida H, Tanaka K, Sugiyama M, Kawazu Y, Tomooka N, Kato K. Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection. BREEDING SCIENCE 2023; 73:269-277. [PMID: 37840980 PMCID: PMC10570884 DOI: 10.1270/jsbbs.22071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/25/2023] [Indexed: 10/17/2023]
Abstract
Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset ("core collection") are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon.
Collapse
Affiliation(s)
- Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Department of Life Science Systems, Technical University of Munich, Emil-Ramann Strasse 2, Freising 85354, Germany
| | - Tran Phuong Dung
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Mst. Naznin Pervin
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Thanh-Thuy Duong
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue City, Vietnam
| | - Odirich Nnennaya Imoh
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Norihiko Tomooka
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| |
Collapse
|
7
|
Tanaka K, Sugiyama M, Shigita G, Murakami R, Duong TT, Aierken Y, Artemyeva AM, Mamypbelov Z, Ishikawa R, Nishida H, Kato K. Melon diversity on the Silk Road by molecular phylogenetic analysis in Kazakhstan melons. BREEDING SCIENCE 2023; 73:219-229. [PMID: 37404344 PMCID: PMC10316308 DOI: 10.1270/jsbbs.22030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 01/16/2023] [Indexed: 07/06/2023]
Abstract
To uncover population structure, phylogenetic relationship, and diversity in melons along the famous Silk Road, a seed size measurement and a phylogenetic analysis using five chloroplast genome markers, 17 RAPD markers and 11 SSR markers were conducted for 87 Kazakh melon accessions with reference accessions. Kazakh melon accessions had large seed with exception of two accessions of weedy melon, Group Agrestis, and consisted of three cytoplasm types, of which Ib-1/-2 and Ib-3 were dominant in Kazakhstan and nearby areas such as northwestern China, Central Asia and Russia. Molecular phylogeny showed that two unique genetic groups, STIa-2 with Ib-1/-2 cytoplasm and STIa-1 with Ib-3 cytoplasm, and one admixed group, STIAD combined with STIa and STIb, were prevalent across all Kazakh melon groups. STIAD melons that phylogenetically overlapped with STIa-1 and STIa-2 melons were frequent in the eastern Silk Road region, including Kazakhstan. Evidently, a small population contributed to melon development and variation in the eastern Silk Road. Conscious preservation of fruit traits specific to Kazakh melon groups is thought to play a role in the conservation of Kazakh melon genetic variation during melon production, where hybrid progenies were generated through open pollination.
Collapse
Affiliation(s)
- Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima Naka, Kita-ku, Okayama, Okayama 700-8530, Japan
| | - Ryoma Murakami
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Thanh-Thuy Duong
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue City, Vietnam
| | - Yasheng Aierken
- Center for Hami Melon, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China
| | - Anna M Artemyeva
- All-Russian Institute of Plant Genetic Resources on the name of N.I.Vavilov (VIR), 42-44 Bolshaya Morskaya Street, Saint Petersburg 190000, Russian Federation
| | - Zharas Mamypbelov
- Kazakhstan Research Institute of Potato and Vegetable Growing LLC, 1 Nauryz Street, Karasay, Almaty 040917, Kazakhstan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima Naka, Kita-ku, Okayama, Okayama 700-8530, Japan
| | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima Naka, Kita-ku, Okayama, Okayama 700-8530, Japan
| |
Collapse
|
8
|
Hernandez CO, Labate J, Reitsma K, Fabrizio J, Bao K, Fei Z, Grumet R, Mazourek M. Characterization of the USDA Cucurbita pepo, C. moschata, and C. maxima germplasm collections. FRONTIERS IN PLANT SCIENCE 2023; 14:1130814. [PMID: 36993863 PMCID: PMC10040574 DOI: 10.3389/fpls.2023.1130814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/22/2023] [Indexed: 06/19/2023]
Abstract
The Cucurbita genus is home to a number of economically and culturally important species. We present the analysis of genotype data generated through genotyping-by-sequencing of the USDA germplasm collections of Cucurbita pepo, C. moschata, and C. maxima. These collections include a mixture of wild, landrace, and cultivated specimens from all over the world. Roughly 1,500 - 32,000 high-quality single nucleotide polymorphisms (SNPs) were called in each of the collections, which ranged in size from 314 to 829 accessions. Genomic analyses were conducted to characterize the diversity in each of the species. Analysis revealed extensive structure corresponding to a combination of geographical origin and morphotype/market class. Genome-wide associate studies (GWAS) were conducted using both historical and contemporary data. Signals were observed for several traits, but the strongest was for the bush (Bu) gene in C. pepo. Analysis of genomic heritability, together with population structure and GWAS results, was used to demonstrate a close alignment of seed size in C. pepo, maturity in C. moschata, and plant habit in C. maxima with genetic subgroups. These data represent a large, valuable collection of sequenced Cucurbita that can be used to direct the maintenance of genetic diversity, for developing breeding resources, and to help prioritize whole-genome re-sequencing.
Collapse
Affiliation(s)
- Christopher O. Hernandez
- Department of Agriculture Nutrition and Food Systems, University of New Hampshire, Durham, NH, United States
| | - Joanne Labate
- Plant Genetic Resource Conservation Unit, United States Department of Agricultural Research Service, Geneva, NY, United States
| | - Kathleen Reitsma
- North Central Regional Plant Introduction Station, Iowa State University, Ames, IA, United States
| | - Jack Fabrizio
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Kan Bao
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY, United States
- U.S. Department of Agriculture-Agriculture Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI, United States
| | - Michael Mazourek
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| |
Collapse
|
9
|
Yu J, Wu S, Sun H, Wang X, Tang X, Guo S, Zhang Z, Huang S, Xu Y, Weng Y, Mazourek M, McGregor C, Renner SS, Branham S, Kousik C, Wechter W, Levi A, Grumet R, Zheng Y, Fei Z. CuGenDBv2: an updated database for cucurbit genomics. Nucleic Acids Res 2022; 51:D1457-D1464. [PMID: 36271794 PMCID: PMC9825510 DOI: 10.1093/nar/gkac921] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/03/2022] [Accepted: 10/06/2022] [Indexed: 01/30/2023] Open
Abstract
The Cucurbitaceae (cucurbit) family consists of about 1,000 species in 95 genera, including many economically important and popular fruit and vegetable crops. During the past several years, reference genomes have been generated for >20 cucurbit species, and variome and transcriptome profiling data have been rapidly accumulated for cucurbits. To efficiently mine, analyze and disseminate these large-scale datasets, we have developed an updated version of Cucurbit Genomics Database. The updated database, CuGenDBv2 (http://cucurbitgenomics.org/v2), currently hosts 34 reference genomes from 27 cucurbit species/subspecies belonging to 10 different genera. Protein-coding genes from these genomes have been comprehensively annotated by comparing their protein sequences to various public protein and domain databases. A novel 'Genotype' module has been implemented to facilitate mining and analysis of the functionally annotated variome data including SNPs and small indels from large-scale genome sequencing projects. An updated 'Expression' module has been developed to provide a comprehensive gene expression atlas for cucurbits. Furthermore, synteny blocks between any two and within each of the 34 genomes, representing a total of 595 pair-wise genome comparisons, have been identified and can be explored and visualized in the database.
Collapse
Affiliation(s)
- Jingyin Yu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shan Wu
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Honghe Sun
- Boyce Thompson Institute, Ithaca, NY 14853, USA,Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Xin Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuemei Tang
- Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Shaogui Guo
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Zhonghua Zhang
- Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China
| | - Sanwen Huang
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong 518124, China
| | - Yong Xu
- National Watermelon and Melon Improvement Center, Beijing Academy of Agricultural and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing 100097, China
| | - Yiqun Weng
- U.S. Department of Agriculture-Agricultural Research Service, Vegetable Crops Research Unit, Madison, WI 53706, USA,Department of Horticulture, University of Wisconsin, Madison, WI 53706, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Cecilia McGregor
- Department of Horticulture, University of Georgia, Athens, GA 30602, USA
| | - Susanne S Renner
- Faculty of Biology, Systematic Botany and Mycology, University of Munich (LMU), 80638 Munich, Germany,Department of Biology, Washington University, Saint Louis, MO 63130, USA
| | - Sandra Branham
- Coastal Research and Educational Center, Clemson University, Charleston, SC 29414, USA
| | - Chandrasekar Kousik
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - W Patrick Wechter
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Amnon Levi
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Vegetable Laboratory, 2700 Savannah Highway, Charleston, SC 29414, USA
| | - Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - Yi Zheng
- Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing 102206, China,Bioinformatics Center, Beijing University of Agriculture, Beijing 102206, China
| | - Zhangjun Fei
- To whom correspondence should be addressed. Tel: +1 607 2543234; Fax: +1 607 2541242;
| |
Collapse
|
10
|
Flores-León A, Peréz Moro C, Martí R, Beltran J, Roselló S, Cebolla-Cornejo J, Picó B. Spanish Melon Landraces: Revealing Useful Diversity by Genomic, Morphological, and Metabolomic Analysis. Int J Mol Sci 2022; 23:ijms23137162. [PMID: 35806170 PMCID: PMC9266967 DOI: 10.3390/ijms23137162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 06/26/2022] [Accepted: 06/26/2022] [Indexed: 12/02/2022] Open
Abstract
Spain is a secondary centre of the diversification of the melon (Cucumis melo L.), with high diversity represented in highly appreciated landraces belonging to the Flexuosus and Ibericus groups. A collection of 47 accessions of Flexuosus, Chate, Piel de Sapo, Tendral, Amarillo, Blanco, and Rochet was analysed using a genotyping-by-sequencing (GBS) approach. A total of 66,971 quality SNPs were identified. Genetic analysis differentiated Ibericus accessions and exotic materials (Ameri, Momordica, Kachri, and Agrestis), while Flexuous accessions shared ancestry between them. Within the Ibericus group, no clear genomic distinction could be identified for the different landraces evaluated, with accessions of different landraces showing high genetic similarity. The morphological characterization confirmed that the external colour and fruit shape had been used as recognition patterns for Spanish melon landraces, but variability within a landrace exists. Differences were found in the sugars and acid and volatile profiles of the materials. Flexuosus and Chate melons at the immature commercial stage accumulated malic acid and low levels of hexoses, while Ibericus melons accumulated high contents of sucrose and citric acid. Specific trends could be identified in the Ibericus landraces. Tendral accumulated low levels of sugars and citric acid and high of malic acid, maintaining higher firmness, Rochet reached higher levels of sugars, and Amarillo tended to lower malic acid contents. Interestingly, high variability was found within landraces for the acidic profile, offering possibilities to alter taste tinges. The main volatile organic compounds (VOCs) in Flexuosus and Chate were aldehydes and alcohols, with clear differences between both groups. In the Ibericus landraces, general trends for VOC accumulation could be identified, but, again, a high level of variation exists. This situation highlights the necessity to develop depuration programs to promote on-farm in situ conservation and, at the same time, offers opportunities to establish new breeding program targets and to take advantage of these sources of variation.
Collapse
Affiliation(s)
- Alejandro Flores-León
- COMAV, Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain; (A.F.-L.); (C.P.M.); (B.P.)
| | - Clara Peréz Moro
- COMAV, Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain; (A.F.-L.); (C.P.M.); (B.P.)
| | - Raul Martí
- Joint Research Unit UJI/UPV—Improvement of Agri-Food Quality, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain;
| | - Joaquin Beltran
- Instituto Universitario de Plaguicidas y Aguas (IUPA), Campus de Riu Sec, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain;
| | - Salvador Roselló
- Joint Research Unit UJI/UPV—Improvement of Agri-Food Quality, Department de Ciències Agràries i del Medi Natural, Universitat Jaume I, Avda. Sos Baynat s/n, 12071 Castellón, Spain;
| | - Jaime Cebolla-Cornejo
- Joint Research Unit UJI/UPV—Improvement of Agri-Food Quality, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain;
- Correspondence:
| | - Belen Picó
- COMAV, Instituto de Conservación y Mejora de la Agrodiversidad, Universitat Politècnica de València, Cno. de Vera, s.n., 46022 València, Spain; (A.F.-L.); (C.P.M.); (B.P.)
| |
Collapse
|