Cargando…

What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima

Since their introduction in Europe, pumpkins (Cucurbita maxima Duch.) have rapidly dispersed throughout the world. This is mainly because of their wide genetic diversity and Plasticity to thrive in a wide range of geographical regions across the world, their high nutritional value and suitability to...

Descripción completa

Detalles Bibliográficos
Autores principales: Reddy, Umesh K., Natarajan, Purushothaman, Abburi, Venkata Lakshmi, Tomason, Yan, Levi, Amnon, Nimmakayala, Padma
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531317/
https://www.ncbi.nlm.nih.gov/pubmed/36204309
http://dx.doi.org/10.3389/fgene.2022.1005158
_version_ 1784801877538373632
author Reddy, Umesh K.
Natarajan, Purushothaman
Abburi, Venkata Lakshmi
Tomason, Yan
Levi, Amnon
Nimmakayala, Padma
author_facet Reddy, Umesh K.
Natarajan, Purushothaman
Abburi, Venkata Lakshmi
Tomason, Yan
Levi, Amnon
Nimmakayala, Padma
author_sort Reddy, Umesh K.
collection PubMed
description Since their introduction in Europe, pumpkins (Cucurbita maxima Duch.) have rapidly dispersed throughout the world. This is mainly because of their wide genetic diversity and Plasticity to thrive in a wide range of geographical regions across the world, their high nutritional value and suitability to integrate with local cuisines, and their long shelf life. Competition for growing the showy type or mammoth-sized pumpkins that produce the largest fruit of the entire plant kingdom has drawn attention. In this study, we used genome-wide single nucleotide polymorphisms to resolve admixture among different pumpkin groups. Also, to resolve population differentiation, genome-wide divergence and evolutionary forces underlying the evolution of mammoth-sized pumpkin. The admixture analysis indicates that the mammoth group (also called Display or Giant) evolved from the hubbard group with genome-wide introgressions from the buttercup group. We archived a set of private alleles underlying fruit development in mammoth group, and resolved haplotype level divergence involved in the evolutionary mechanisms. Our genome-wide association study identified three major allelic effects underlying various fruit-size genes in this study. For fruit weight, a missense variant in the homeobox-leucine zipper protein ATHB-20-like (S04_18528409) was significantly associated (false discovery rate = 0.000004) with fruit weight, while high allelic effect was consistent across the 3 years of the study. A cofactor (S08_217549) on chromosome 8 is strongly associated with fruit length, having superior allelic effect across the 3 years of this study. A missense variant (S10_4639871) on translocation protein SEC62 is a cofactor for fruit diameter. Several known molecular mechanisms are likely controlling giant fruit size, including endoreduplication, hormonal regulation, CLV-WUS signaling pathway, MADS-box family, and ubiquitin-proteasome pathway. This study provides a general framework for the evolutionary relationship among horticulture groups of C. maxima and elucidates the origins of rare variants contributing to the giant pumpkin fruit size.
format Online
Article
Text
id pubmed-9531317
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-95313172022-10-05 What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima Reddy, Umesh K. Natarajan, Purushothaman Abburi, Venkata Lakshmi Tomason, Yan Levi, Amnon Nimmakayala, Padma Front Genet Genetics Since their introduction in Europe, pumpkins (Cucurbita maxima Duch.) have rapidly dispersed throughout the world. This is mainly because of their wide genetic diversity and Plasticity to thrive in a wide range of geographical regions across the world, their high nutritional value and suitability to integrate with local cuisines, and their long shelf life. Competition for growing the showy type or mammoth-sized pumpkins that produce the largest fruit of the entire plant kingdom has drawn attention. In this study, we used genome-wide single nucleotide polymorphisms to resolve admixture among different pumpkin groups. Also, to resolve population differentiation, genome-wide divergence and evolutionary forces underlying the evolution of mammoth-sized pumpkin. The admixture analysis indicates that the mammoth group (also called Display or Giant) evolved from the hubbard group with genome-wide introgressions from the buttercup group. We archived a set of private alleles underlying fruit development in mammoth group, and resolved haplotype level divergence involved in the evolutionary mechanisms. Our genome-wide association study identified three major allelic effects underlying various fruit-size genes in this study. For fruit weight, a missense variant in the homeobox-leucine zipper protein ATHB-20-like (S04_18528409) was significantly associated (false discovery rate = 0.000004) with fruit weight, while high allelic effect was consistent across the 3 years of the study. A cofactor (S08_217549) on chromosome 8 is strongly associated with fruit length, having superior allelic effect across the 3 years of this study. A missense variant (S10_4639871) on translocation protein SEC62 is a cofactor for fruit diameter. Several known molecular mechanisms are likely controlling giant fruit size, including endoreduplication, hormonal regulation, CLV-WUS signaling pathway, MADS-box family, and ubiquitin-proteasome pathway. This study provides a general framework for the evolutionary relationship among horticulture groups of C. maxima and elucidates the origins of rare variants contributing to the giant pumpkin fruit size. Frontiers Media S.A. 2022-09-20 /pmc/articles/PMC9531317/ /pubmed/36204309 http://dx.doi.org/10.3389/fgene.2022.1005158 Text en Copyright © 2022 Reddy, Natarajan, Abburi, Tomason, Levi and Nimmakayala. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Reddy, Umesh K.
Natarajan, Purushothaman
Abburi, Venkata Lakshmi
Tomason, Yan
Levi, Amnon
Nimmakayala, Padma
What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima
title What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima
title_full What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima
title_fullStr What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima
title_full_unstemmed What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima
title_short What makes a giant fruit? Assembling a genomic toolkit underlying various fruit traits of the mammoth group of Cucurbita maxima
title_sort what makes a giant fruit? assembling a genomic toolkit underlying various fruit traits of the mammoth group of cucurbita maxima
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9531317/
https://www.ncbi.nlm.nih.gov/pubmed/36204309
http://dx.doi.org/10.3389/fgene.2022.1005158
work_keys_str_mv AT reddyumeshk whatmakesagiantfruitassemblingagenomictoolkitunderlyingvariousfruittraitsofthemammothgroupofcucurbitamaxima
AT natarajanpurushothaman whatmakesagiantfruitassemblingagenomictoolkitunderlyingvariousfruittraitsofthemammothgroupofcucurbitamaxima
AT abburivenkatalakshmi whatmakesagiantfruitassemblingagenomictoolkitunderlyingvariousfruittraitsofthemammothgroupofcucurbitamaxima
AT tomasonyan whatmakesagiantfruitassemblingagenomictoolkitunderlyingvariousfruittraitsofthemammothgroupofcucurbitamaxima
AT leviamnon whatmakesagiantfruitassemblingagenomictoolkitunderlyingvariousfruittraitsofthemammothgroupofcucurbitamaxima
AT nimmakayalapadma whatmakesagiantfruitassemblingagenomictoolkitunderlyingvariousfruittraitsofthemammothgroupofcucurbitamaxima