Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima)
Atlantic Giant (AG) pumpkin (Cucurbita maxima) produces the world’s largest fruit. Elucidating the molecular mechanism of AG fruit formation is of scientific and practical importance. In this research, genome-wide resequencing of an F2 population produced by a cross between AG and its small-fruit an...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2022-07-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.942004/full |
| _version_ | 1811288997098422272 |
|---|---|
| author | Liu Pan Min Wang Yating Yang Chen Chen Haibo Dai Zhiping Zhang Bing Hua Minmin Miao Minmin Miao Minmin Miao |
| author_facet | Liu Pan Min Wang Yating Yang Chen Chen Haibo Dai Zhiping Zhang Bing Hua Minmin Miao Minmin Miao Minmin Miao |
| author_sort | Liu Pan |
| collection | DOAJ |
| description | Atlantic Giant (AG) pumpkin (Cucurbita maxima) produces the world’s largest fruit. Elucidating the molecular mechanism of AG fruit formation is of scientific and practical importance. In this research, genome-wide resequencing of an F2 population produced by a cross between AG and its small-fruit ancestor Hubbard was used to identify quantitative trait loci (QTLs) and candidate genes. Transgressive segregation of fruit size-related traits was observed in the F2 population, suggesting that fruit size was a quantitative trait controlled by multiple genes. A genetic map with an average physical distance of 154 kb per marker was constructed, and 13 QTLs related to fruit size were identified using bin-map construction. RNA sequencing analysis revealed that pathways associated with assimilate accumulation into the fruit, including carbohydrate metabolism, were significantly enriched in differentially expressed genes. According to the predicted impact of mutation on the biological function of certain proteins, 13 genes were selected as candidate genes associated with fruit size, among which two phytohormone-related genes, CmaCh17G011340 (a flavin-containing monooxygenase) and CmaCh04G029660 (a leucine-rich repeat protein kinase) were chosen for further investigation. Finally, one insertion-deletion (inDel) and three single nucleotide polymorphisms (SNPs) were successfully transformed to Kompetitive Allele-Specific PCR (KASP) markers. The novel QTLs and candidate genes identified provide insights into the genetic mechanism of large fruit formation of AG, and the genetic map and tightly linked KASP markers developed in this study can be employed for marker-assisted breeding to alter fruit size of C. maxima. |
| first_indexed | 2024-04-13T03:47:08Z |
| format | Article |
| id | doaj.art-a437b8cc9f464d9d92e4d4c8debd68f2 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T03:47:08Z |
| publishDate | 2022-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-a437b8cc9f464d9d92e4d4c8debd68f22022-12-22T03:03:59ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-07-011310.3389/fpls.2022.942004942004Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima)Liu Pan0Min Wang1Yating Yang2Chen Chen3Haibo Dai4Zhiping Zhang5Bing Hua6Minmin Miao7Minmin Miao8Minmin Miao9College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaCollege of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaCollege of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaCollege of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaCollege of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaCollege of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaCollege of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaCollege of Horticulture and Plant Protection, Yangzhou University, Yangzhou, ChinaJoint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, ChinaKey Laboratory of Plant Functional Genomics of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, ChinaAtlantic Giant (AG) pumpkin (Cucurbita maxima) produces the world’s largest fruit. Elucidating the molecular mechanism of AG fruit formation is of scientific and practical importance. In this research, genome-wide resequencing of an F2 population produced by a cross between AG and its small-fruit ancestor Hubbard was used to identify quantitative trait loci (QTLs) and candidate genes. Transgressive segregation of fruit size-related traits was observed in the F2 population, suggesting that fruit size was a quantitative trait controlled by multiple genes. A genetic map with an average physical distance of 154 kb per marker was constructed, and 13 QTLs related to fruit size were identified using bin-map construction. RNA sequencing analysis revealed that pathways associated with assimilate accumulation into the fruit, including carbohydrate metabolism, were significantly enriched in differentially expressed genes. According to the predicted impact of mutation on the biological function of certain proteins, 13 genes were selected as candidate genes associated with fruit size, among which two phytohormone-related genes, CmaCh17G011340 (a flavin-containing monooxygenase) and CmaCh04G029660 (a leucine-rich repeat protein kinase) were chosen for further investigation. Finally, one insertion-deletion (inDel) and three single nucleotide polymorphisms (SNPs) were successfully transformed to Kompetitive Allele-Specific PCR (KASP) markers. The novel QTLs and candidate genes identified provide insights into the genetic mechanism of large fruit formation of AG, and the genetic map and tightly linked KASP markers developed in this study can be employed for marker-assisted breeding to alter fruit size of C. maxima.https://www.frontiersin.org/articles/10.3389/fpls.2022.942004/fullAtlantic Giantfruit sizegenome-wide resequencingKASP markerCucurbita maxima |
| spellingShingle | Liu Pan Min Wang Yating Yang Chen Chen Haibo Dai Zhiping Zhang Bing Hua Minmin Miao Minmin Miao Minmin Miao Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima) Frontiers in Plant Science Atlantic Giant fruit size genome-wide resequencing KASP marker Cucurbita maxima |
| title | Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima) |
| title_full | Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima) |
| title_fullStr | Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima) |
| title_full_unstemmed | Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima) |
| title_short | Whole-genome resequencing identified QTLs, candidate genes and Kompetitive Allele-Specific PCR markers associated with the large fruit of Atlantic Giant (Cucurbita maxima) |
| title_sort | whole genome resequencing identified qtls candidate genes and kompetitive allele specific pcr markers associated with the large fruit of atlantic giant cucurbita maxima |
| topic | Atlantic Giant fruit size genome-wide resequencing KASP marker Cucurbita maxima |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.942004/full |
| work_keys_str_mv | AT liupan wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT minwang wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT yatingyang wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT chenchen wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT haibodai wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT zhipingzhang wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT binghua wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT minminmiao wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT minminmiao wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima AT minminmiao wholegenomeresequencingidentifiedqtlscandidategenesandkompetitiveallelespecificpcrmarkersassociatedwiththelargefruitofatlanticgiantcucurbitamaxima |