A natural mutation of the NST1 gene arrests secondary cell wall biosynthesis in the seed coat of a hull-less pumpkin accession

Abstract

Hull-less pumpkins (Cucurbita pepo L.) are naturally occurring novel variants known as oilseed or naked-seeded pumpkins, and are characterized by the absence of a normal lignified seed coat. Due to a specialized seed coat structure, these variants serve as a good model for studying seed coat formation and simplify the processing of pumpkin seeds. However, causal genes for this hull-less trait still remain unknown. Here, by Bulked Segregant Analysis (BSA) and fine mapping, we found that mutation of a single gene, NAC SECONDARY WALL THICKENING PROMOTING FACTOR 1 (NST1), accounts for the hull-less trait. A 14-bp sequence insertion in the CpNST1 gene causes premature termination of CpNST1 translation, leading to lack of secondary cell wall (SCW) biosynthesis in hull-less seed coats. In situ hybridization analysis provided further evidence for the role of CpNST1 in pumpkin seed coat SCW biosynthesis. Interestingly, through secondary cell wall compositional analysis, we found that the main SCW components differed among cell layers in the seed coat. RNA-seq analysis indicated an upstream role of CpNST1 in the SCW biosynthesis network. Collectively, our findings provide mechanistic insight into seed coat SCW biosynthesis, and a target gene as well for breeders to introduce this hull-less trait for commercial exploitation.

Identification of the egusi seed trait locus (eg) and its suppressor gene associated with the thin seed coat trait in watermelon

“…Based on the watermelon germplasms preserved in the National Mid-Term Genebank for Watermelon and Melon (Zhengzhou, China), egusi watermelon with a typical egusi type seed coat is shown in Figure 1 . The type 1 class of seeds with thin seed coats and flat edges looks morphologically similar to the hull-less seeds in pumpkin ( Lyu et al., 2022 ), which will be the focus of our research in the present study. The hull-less trait is an important trait in seed crops.…”

“…The partial egusi seed type in watermelon (unique egusi seed type in the present study) is similar to the hull-less trait in seed crops. Previous studies showed that one major gene, a minor gene with modifiers, or a polygenic model controlled the hull-less trait in other seed crops, such as pumpkin ( Chahal et al., 2022 ; Lyu et al., 2022 ), barley ( Taketa et al., 2008 ), oil palm ( Singh et al., 2013 ), and maize ( Wang et al., 2005 ). In the present study, two genes with inhibitory epistasis were found to be responsible for egusi seeds in watermelon as evidenced by the F 2 ratio (13:3) and confirmed by the phenotype and genotype in the BC 1 F 2 population.…”

“…An ethylene response factor family gene regulating a lipid biosynthesis pathway controls the covered/naked caryopsis phenotype in barley ( Taketa et al., 2008 ). A single gene, NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) , accounts for the hull-less trait in pumpkin ( Lyu et al., 2022 ). Previous studies suggested that “naked-seed” pumpkin is the result of reduced cellulose and lignin contents in the hull-less seed coat at seed maturation ( Bezold et al., 2005 ; Lyu et al., 2022 ).…”

“…The hull-less trait is usually controlled by a single or several genes. Both watermelon and pumpkin belong to the Cucurbitaceae family, so pumpkin is taken as an example: the hull-less pumpkin testa is the result of a single recessive gene with or without other modifying genes ( Chahal et al., 2022 ; Lyu et al., 2022 ).…”

“…Edible seeds of other cucurbits, such as pumpkin, squash, and bottle gourd ( Idouraine et al., 1996 ; Chahal et al., 2022 ; Lyu et al., 2022 ), are also nutritious and form a part of the diet. Watermelon with edible egusi seeds and red, sweet, and edible flesh, like the soft seeds in pomegranate ( Luo et al., 2020 ), would be extremely convenient for watermelon producers and consumers.…”