AUTHOR=Kaur Barinder , Garcha Karmvir Singh , Bhatia Dharminder , Khosa Jiffinvir Singh , Sharma Madhu , Mittal Amandeep , Verma Neha , Dhatt Ajmer Singh 

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

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.948106

DOI=10.3389/fpls.2022.948106

ISSN=1664-462X

ABSTRACT=<p>The hull-less pumpkin (<italic>Cucurbita pepo</italic>) seed does not require de-hulling before use for human consumption, as a result highly preferred by the oil, nut, and baking industries. In hull-less seeds, a single recessive gene is responsible for the absence of outer thick seed coat layers; however, the genomic region and gene(s) controlling the trait are unclear to date. In this study, four crosses attempted to derive F<sub>2</sub> and backcross populations confirmed the single recessive gene inheritance of hull-less seed trait in populations adapted to the sub-tropical climate. The candidate genomic region for hull-less seed trait was identified through the BSA-QTLseq approach using bulks of F<sub>2:3</sub> progenies from a cross of HP111 (hulled) and HLP36 (hull-less). A novel genomic region on chromosome 12 ranging from 1.80 to 3.86 Mb was associated with the hull-less seed trait. The re-sequencing data identified a total of 396 SNPs within this region and eight were successfully converted into polymorphic KASP assays. The genotyping of segregating F<sub>2</sub> (<italic>n</italic> = 160) with polymorphic KASP assays resulted in a 40.3 cM partial linkage map and identified Cp_3430407 (10 cM) and Cp_3498687 (16.1 cM) as flanking markers for hull-less locus (<italic>Cphl-1</italic>). These flanking markers correspond to the 68.28 kb region in the reference genome, and the marker, Cp_3430407 successfully predicted the genotype in 93.33% of the <italic>C. pepo</italic> hull-less germplasm lines, thus can be used for marker-assisted selection in parents polymorphic for the hull-less seed trait. The <italic>Cphl-1</italic>-linked genomic region (2.06 Mb) encompasses a total of 182 genes, including secondary cell wall and lignin biosynthesis-related transcriptional factors <italic>viz</italic>., “NAC” (<italic>Cp4.1LG12g04350</italic>) and “MYB” (<italic>Cp4.1LG12g03120</italic>). These genes were differentially expressed in the seeds of hulled and hull-less genotypes, and therefore could be the potential candidate genes governing the hull-less seed trait in pumpkin.</p>