Long‐read genome assembly and genetic architecture of fruit shape in the bottle gourd

Abstract

SUMMARY The bottle gourd (Lagenaria siceraria, Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long‐read‐based, high‐quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390‐fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one‐step geometric morphometrics‐based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well‐known and newly identified fruit shape genes, including SUN, OFP, AP2 and auxin transporters, were comapped with bottle gourd QTLs.

Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd

“…In this study, we developed a core collection of 102 accessions that represent 100% of the bottle gourd collections in China (Table 5 and Figure 6). Previous studies have revealed weak population stratification and low diversity in bottle gourd germplasm collections, which are generally independent of the site of collection (Yetişir et al, 2008;Xu et al, 2011Xu et al, , 2014Xu et al, , 2021. Taking into consideration the factors of suitable size, phenotype, and unique agronomic traits, we augmented our original core collection with an additional 48 inbred lines, thereby establishing a final core collection containing 150 bottle gourd inbred lines.…”

“…(2n = 2x = 22), also known as calabash or long melon, is a cultivated vegetable, medicinal plant, decorative cucurbit, and grafting rootstock belonging to the Cucurbitaceae family, together with other major cucurbit crops, including cucumber ( Cucumis sativus L.), melon ( Cucumis melo L.), and watermelon ( Citrullus lanatus L.) ( Heiser, 1979 ; Beevy and Kuriachan, 1996 ; Erickson et al, 2005 ; Morimoto et al, 2005 ). Recently, a high-quality bottle gourd reference genome (contig N50 = 11.2 Mb, scaffold N50 = 28.4 Mb) of 297 Mb was released for the Chinese landrace “Hangzhou Gourd” ( Xu et al, 2021 ).…”

“…Although originating from Africa, the bottle gourd was in use by humans in east Asia, the Americas, Europe, and the South Pacific ( Erickson et al, 2005 ; Schlumbaum and Vandorpe, 2012 ; Kistler et al, 2014 ). Bottle gourd populations exhibit a tremendous diversity in fruit shape ( Heiser, 1979 ; Morimoto and Mvere, 2004 ; Xu et al, 2014 , 2021 ), based on which the bottle gourd populations are consistently grouped rather than the geographical origin ( Xu et al, 2011 ; Mladenovic et al, 2012 ; Yildiz et al, 2015 ). Bottle gourd germplasm is preserved in several seed banks and is used in various research by different institutions across the world ( Morimoto et al, 2005 ; Achigan-Dako et al, 2008 ; Gurcan et al, 2015 ; Xu et al, 2021 ).…”

Table_1.XLSX

“…As a reference for SNP discovery, we used the Chinese landrace bottle gourd "HZ gourd" (Xu et al, 2021). Based on the SNP polymorphism information content (PIC) values of the genotypes of the 20 bottle gourd representatives that were resequenced in a recently published study (Xu et al, 2021), we selected SNPs for identification by KASP assays on another 22 distantly related accessions that were selected from the 206 bottle gourd germplasm collections. After eliminating lowquality and low-discriminatory SNPs, high-quality SNPs were selected for core SNP marker screening of the 206 bottle gourd germplasm collections.…”

“…Although originating from Africa, the bottle gourd was in use by humans in east Asia, the Americas, Europe, and the South Pacific (Erickson et al, 2005;Schlumbaum and Vandorpe, 2012;Kistler et al, 2014). Bottle gourd populations exhibit a tremendous diversity in fruit shape (Heiser, 1979;Morimoto and Mvere, 2004;Xu et al, 2014Xu et al, , 2021, based on which the bottle gourd populations are consistently grouped rather than the geographical origin (Xu et al, 2011;Mladenovic et al, 2012;Yildiz et al, 2015). Bottle gourd germplasm is preserved in several seed banks and is used in various research by different institutions across the world (Morimoto et al, 2005;Achigan-Dako et al, 2008;Gurcan et al, 2015;Xu et al, 2021).…”