Quantitative Trait Loci (QTL) Analysis of Fruit and Agronomic Traits of Tropical Pumpkin (Cucurbita moschata) in an Organic Production System

Angel R Del Valle Echevarria,Tia Silvasy,Sarah Moore,Theodore J K Radovich,Alexandra Campbell,Michael B Kantar

doi:10.3390/horticulturae6010014

Angel R Del Valle Echevarria, Tia Silvasy + Show 4 more

Open Access

https://doi.org/10.3390/horticulturae6010014

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Abstract

Interest in the development of organically grown vegetable crops has risen over the past decades due to consumer preferences. However, most crops that have desirable consumer traits have been bred in conventional growing conditions, and their transfer to an organic setting is challenging. Here, the organically grown Hawaiian pumpkin (Cucurbita moschata) accession ‘Shima’ was crossed with the conventionally grown Puerto Rican variety ‘Taina Dorada’ to develop a backcross (BC1) population, where ‘Shima’ was the recurrent parent. A total of 202 BC1 (‘Shima’ X F1) progenies were planted in a certified organic field, and twelve traits were evaluated. We used genotype-by-sequencing (GBS) to identify the Quantitative Trait Loci (QTL) associated with insect tolerance along with commercially desirable traits. A total of 1582 single nucleotide polymorphisms (SNPs) were identified, from which 711 SNPs were used to develop a genetic map and perform QTL mapping. Reads associated with significant QTLs were aligned to the publicly available Cucurbita moschata genome and identified several markers linked to genes that have been previously reported to be associated with that trait in other crop systems, such as melon (Cucumis melo L.). This research provides a resource for marker-assisted selection (MAS) efforts in Cucurbita moschata, as well as serving as a model study to improve cultivars that are transitioning from a conventional to an organic setting.

Highlights

Conventional breeding efforts have focused on selecting in high levels of inorganic fertilizer and crop protection inputs
CmoCh15G001520, a clathrin heavy chain protein parallel, Pumpkin_164349, which our study showed to be associated with pickleworm tolerance, encoding gene CmoCh15G001520, orthologous to MELO3C008306 that haschain been observed to be upregulated in Fusariumto aligns with a clathrin heavy protein encoding gene orthologous infections
We focused on molecular pumpkin breeding from conventional to organic farming in

Summary

Introduction

Conventional breeding efforts have focused on selecting in high levels of inorganic fertilizer and crop protection inputs. The use of molecular markers has become a viable way to identify genetic loci associated with desired phenotypes in parallel with successful establishment in an organic setting [4,5]. Most of these approaches focus on major crops such as wheat [6], sweet corn [4], tomato [7], and barley [8], Horticulturae 2020, 6, 14; doi:10.3390/horticulturae6010014 www.mdpi.com/journal/horticulturae

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