A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita pepo L.

Abstract

As one of the earliest domesticated species, Cucurbita pepo (including squash and pumpkin) is rich in phenotypic polymorphism and has huge economic value. In this research, using 1660 expressed sequence tags-simple sequence repeats (EST-SSRs) and 632 genomic simple sequence repeats (gSSRs), we constructed the highest-density EST-SSR-based genetic map in Cucurbita genus, which spanned 2199.1 cM in total and harbored 623 loci distributed in 20 linkage groups. Using this map as a bridge, the two previous gSSR maps were integrated by common gSSRs and the corresponding relationships around chromosomes in three sets of genomes were also collated. Meanwhile, one large segmental inversion that existed between our map and the C. pepo genome was detected. Furthermore, three Quantitative Trait Loci (QTLs) of the dwarf trait (gibberellin-sensitive dwarf type) in C. pepo were located, and the candidate region that covered the major QTL spanned 1.39 Mb, which harbored a predicted gibberellin 2-β-oxidase gene. Considering the rich phenotypic polymorphism, the important economic value in the Cucurbita genus species and several advantages of the SSR marker were identified; thus, this high-density EST-SSR-based genetic map will be useful in Pumpkin and Squash breeding work in the future.

Genetic relationships among Cucurbita pepo ornamental gourds based on EST-SSR markers

“…SSR analysis. All the EST-SSR markers for the Cucurbita pepo used during the study were established by Xiang et al (2018) using transcriptome data for C. pepo in the Cucurbit Genomics Database (http://www.icugi.org). The EST-SSR markers with polymorphic alleles (at least two different allelic variants among all the accessions) were selected for genotyping in this study.…”

Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima

“…Young leaf samples of P 1 , P 2 , F 1 , and all of the F 2 plants with unique number were collected and frozen in liquid nitrogen. DNA extraction was performed as described by Xiang et al [ 42 ]. For RNA extraction, the sample of seed coat were collected after removing the pulp in different development stages (0, 7, 14, 21, 28, 35, 42 DPA).…”

“…Improvements of whole genome sequences and high-density genetic maps have promoted the precision of genomic data in Cucurbita and support a better foundation for the research and application of candidate genes in Cucurbita species [ 36 , 37 , 38 , 39 , 40 , 41 ]. With effective utilization of molecular markers and genetic map resources, QTLs for many agronomic traits and candidate genes have been identified and applicated accordingly in breeding selection [ 42 , 43 , 44 , 45 , 46 ]. Some QTLs of seed trait such as seed size, seed width, and seed yields have been identified in Cucurbita maxima and candidate genes are precited [ 10 , 47 ].…”

Obtaining doubled haploids of Cucurbita pepo L.

“…Появившиеся в последнее время публикации по изучению генетического разнообразия C.pepo с использованием молекулярных маркеров, большое количество разработанных праймеров и построенная генетическая карта этого вида [136,137], не оставляет сомнения, что в ближайшее время в протоколы получения удвоенных гаплоидов у различных разновидностей C.pepo будет обязательно включен этап тестирования с использованием, молекулярных маркеров, поскольку только с его помощью можно подтвердить происхождение полученных растений-регенерантов.…”