AUTHOR=Liu Lili , Gan Yaqin , Luo Jianning , Li Junxing , Zheng Xiaoming , Gong Hao , Liu Xiaoxi , Deng Liting , Zhao Gangjun , Wu Haibin 

TITLE=QTL mapping reveals candidate genes for main agronomic traits in Luffa based on a high-resolution genetic map

JOURNAL=Frontiers in Plant Science

VOLUME=13

YEAR=2022

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2022.1069618

DOI=10.3389/fpls.2022.1069618

ISSN=1664-462X

ABSTRACT=<p><italic>Luffa</italic> is an important medicinal and edible vegetable crop of Cucurbitaceae. Strong heterosis effects and strikingly complementary characteristics were found between the two domesticated <italic>Luffa</italic> cultivars, <italic>Luffa acutangula</italic> and <italic>Luffa cylindrica</italic>. To explore the genetic basis underlying their important agronomic traits, we constructed the first interspecific high-density genetic linkage map using a BC<sub>1</sub> population of 110 lines derived from a cross between S1174 (<italic>Luffa acutangula</italic>) and P93075 (<italic>Luffa cylindrica</italic>). The map spanned a total of 2246.74 cM with an average distance of 0.48 cM between adjacent markers. Thereafter, a large-scale field-based quantitative trait loci (QTLs) mapping was conducted for 25 important agronomic traits and 40 significant genetic loci distributed across 11 chromosomes were detected. Notably, a vital QTL (<italic>qID2</italic>) located on chromosome 9 with a minimum distance of 23 kb was identified to be responsible for the internode diameter and explained 11% of the phenotypic variation. <italic>Lac09g006860</italic> (<italic>LacCRWN3</italic>), encoding a nuclear lamina protein involved in the control of nuclear morphology, was the only gene harbored in <italic>qID2</italic>. Sequence alignment showed completely different promoter sequences between the two parental alleles of <italic>LacCRWN3</italic> except for some nonsynonymous single nucleotide polymorphisms (SNPs) in exons, and the expression level in thick-stem P93075 was distinctively higher than that in thin-stem S1174. According to the natural variation analysis of a population of 183 inbred lines, two main haplotypes were found for <italic>LacCRWN3</italic>: the P93075-like and S1174-like, with the former haplotype lines exhibiting significantly thicker internode diameters than those of the latter haplotype lines. It showed that <italic>LacCRWN3</italic>, as the only CRWN3 gene in Cucurbitaceae, was the most likely candidate gene regulating the internode diameter of <italic>Luffa</italic>. Our findings will be beneficial for deciphering the molecular mechanism of key phenotypic traits and promoting maker-assisted breeding in <italic>Luffa</italic>.</p>