Genomic Position and Markers Associated with the Hull-Less Seed Trait in Pumpkin

Abstract

Pumpkin (Cucurbita pepo) seeds are nutritious and valued as a source of vegetable oil, protein, healthy fatty acids, and minerals. Pumpkin seeds that are naturally devoid of the seedcoat (hull-less) are preferred by the industry as they eliminate the need for de-hulling prior to use. A single recessive gene, designated as n or h, controls the hull-less seed trait in pumpkin. Visual selection for the trait is easy, however, it is resource intensive when applied to large breeding populations. High throughput genotyping assays can aid in the identification of suitable individuals in segregating populations through marker-assisted selection. In the current study, the QTL-seq approach was used to identify genetic loci, SNP markers and candidate genes associated with the hull-less trait in a segregating F2 population (n = 143) derived from a cross between Kakai (hull-less) × Table Gold Acorn (hulled). The segregation of the hull-less trait in the F2 population fit a 3:1 ratio (p < 0.05). QTL-seq analysis detected a single QTL on chromosome 12 (Qtlhull-less-C12) which was significantly associated with the hull-less trait in C. pepo. Twenty-eight SNPs were genotyped in the population, two among which (Ch12_3412046 and Ch12_3417142) were significantly associated (p < 0.05) with the hull-less trait in cultivars and accessions of diverse genetic background. Several candidate genes fall within the Qtlhull-less-C12 interval, among them is the No Apical meristem (NAC) domain-containing protein and a Fiber Protein fb11 gene involved in lignin accumulation and cell wall deposition across plant species, respectively. The findings of this study will facilitate the marker-assisted selection for the hull-less seed trait in pumpkin and further our understanding of the functional mechanisms underlying the trait across cucurbit crops.

Interspecific hybridization for transfer of hull-less seed trait from Cucurbita pepo to C. moschata

“…In support to this, our recently published manuscript 22 identified a candidate genomic region linked to hull-less seed trait ranging from 1.80 to 3.86 Mb on chromosome 12 of C. pepo genome and also reported a linked KASP marker. Similar results are also reported by two other recently published studies in C. pepo 23 , 24 . Further, BLASTn results of polymorphic SSR markers with C. pepo (Zucchini) genome revealed that only CMTp182 had the significant hits on chromosome 12 in between the identified candidate genomic region (CMTp182 Forward: 2220598–2220615 and CMTp182 Reverse: 2220732–2220713).…”

“…These results are similar to the previous reports in C. pepo by Stuart 40 , Zraidi et al 41 and Lelley et al 3 . More recently, along with monogenic recessive inheritance, hull-less seed trait has been mapped to chromosome 12 of C. pepo genome with 'NST1' (Cp4.1Lg12g04350) as the putative candidate gene [22][23][24] . However, segregation distortion observed in Family IV, might be due to incomplete representation of whole F 2 population in chi square analysis.…”

Identification of single major QTL and candidate gene(s) governing hull-less seed trait in pumpkin

“…A KASP assay viz ., Cp_3430407 can be utilized for MAS with 93.33% accuracy in hull-less germplasm of C. pepo . The physical positions of this KASP assay are also close to recently identified SNP markers (Ch12_3412046 and Ch12_3417142) reported by Meru et al ( 2022 ).…”

“…A KASP assay viz., Cp_3430407 can be utilized for MAS with 93.33% accuracy in hull-less germplasm of C. pepo. The physical positions of this KASP assay are also close to recently identified SNP markers (Ch12_3412046 and Ch12_3417142) reported by Meru et al (2022). The molecular mechanism of cell wall lignification has been well-studied in Arabidopsis, and over the years, this knowledge has been translated to understand the lignification mechanism in crops (Wang and Dixon, 2012;Barros et al, 2015).…”

“…The BLAST results of the linked SSR markers (CMTm239, CMTp182) from this study revealed significant hits on chromosome 12 of the C. pepo genome, as of the identified region in our study. While we were preparing this manuscript, Meru et al ( 2022 ) identified a large genomic region of 4.43 Mb (1.25–5.68 Mb) on chromosome 12 for the hull-less seed trait; however, in our study, it was narrowed down to ~2 Mb (1.80–3.86 Mb), which might be due to higher number of individuals used for bulk construction.…”