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QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes

Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a...

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Autores principales: Oren, Elad, Tzuri, Galil, Dafna, Asaf, Rees, Evan R, Song, Baoxing, Freilich, Shiri, Elkind, Yonatan, Isaacson, Tal, Schaffer, Arthur A, Tadmor, Yaakov, Burger, Joseph, Buckler, Edward S, Gur, Amit
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8968493/
https://www.ncbi.nlm.nih.gov/pubmed/35043206
http://dx.doi.org/10.1093/hr/uhab081
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author Oren, Elad
Tzuri, Galil
Dafna, Asaf
Rees, Evan R
Song, Baoxing
Freilich, Shiri
Elkind, Yonatan
Isaacson, Tal
Schaffer, Arthur A
Tadmor, Yaakov
Burger, Joseph
Buckler, Edward S
Gur, Amit
author_facet Oren, Elad
Tzuri, Galil
Dafna, Asaf
Rees, Evan R
Song, Baoxing
Freilich, Shiri
Elkind, Yonatan
Isaacson, Tal
Schaffer, Arthur A
Tadmor, Yaakov
Burger, Joseph
Buckler, Edward S
Gur, Amit
author_sort Oren, Elad
collection PubMed
description Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines “Dulce” (reticulatus, climacteric) and “Tam Dew” (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits.
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spelling pubmed-89684932022-03-31 QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes Oren, Elad Tzuri, Galil Dafna, Asaf Rees, Evan R Song, Baoxing Freilich, Shiri Elkind, Yonatan Isaacson, Tal Schaffer, Arthur A Tadmor, Yaakov Burger, Joseph Buckler, Edward S Gur, Amit Hortic Res Article Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation. Using Recombinant Inbred Lines (RILs) population derived from the parental lines “Dulce” (reticulatus, climacteric) and “Tam Dew” (inodorus, non-climacteric) that vary in earliness and ripening traits, we mapped QTLs for ethylene emission, fruit firmness and days to flowering and maturity. To further annotate the main QTL intervals and identify candidate genes, we used Oxford Nanopore long-read sequencing in combination with Illumina short-read resequencing, to assemble the parental genomes de-novo. In addition to 2.5 million genome-wide SNPs and short InDels detected between the parents, we also highlight here the structural variation between these lines and the reference melon genome. Through systematic multi-layered prioritization process, we identified 18 potential polymorphisms in candidate genes within multi-trait QTLs. The associations of selected SNPs with earliness and ripening traits were further validated across a panel of 177 diverse melon accessions and across a diallel population of 190 F1 hybrids derived from a core subset of 20 diverse parents. The combination of advanced genomic tools with diverse germplasm and targeted mapping populations is demonstrated as a way to leverage forward genetics strategies to dissect complex horticulturally important traits. Oxford University Press 2022-01-19 /pmc/articles/PMC8968493/ /pubmed/35043206 http://dx.doi.org/10.1093/hr/uhab081 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nanjing Agricultural University https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Article
Oren, Elad
Tzuri, Galil
Dafna, Asaf
Rees, Evan R
Song, Baoxing
Freilich, Shiri
Elkind, Yonatan
Isaacson, Tal
Schaffer, Arthur A
Tadmor, Yaakov
Burger, Joseph
Buckler, Edward S
Gur, Amit
QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes
title QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes
title_full QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes
title_fullStr QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes
title_full_unstemmed QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes
title_short QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes
title_sort qtl mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported by de novo assembly of their parental genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8968493/
https://www.ncbi.nlm.nih.gov/pubmed/35043206
http://dx.doi.org/10.1093/hr/uhab081
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