Chasing breeding footprints through structural variations inCucumis meloand wild relatives

Abstract

Cucumis melo (melon or muskmelon) is an important crop in the family of the Cucurbitaceae. Melon is cross pollinated and domesticated at several locations throughout the breeding history, resulting in highly diverse genetic structure in the germplasm. Yet, the relations among the groups and cultivars are still incomplete. We shed light on the melonbreeding history, analyzing structural variations ranging from 50 bp up to 100 kb, identified from whole genome sequences of 100 selected melon accessions and wild relatives. Phylogenetic trees based on SV types completely resolve cultivars and wild accessions into two monophyletic groups and clustering of cultivars largely correlates with their geographic origin. Taking into account morphology, we found six mis-categorized cultivars. Unique inversions are more often shared between cultivars, carrying advantageous genes and do not directly originate from wild species. Approximately 60% of the inversion breaks carry a long poly A/T motif, and following observations in other plant species, suggest that inversions in melon likely resulted from meiotic recombination events. We show that resistance genes in the linkage V region are expanded in the cultivar genomes compared to wild relatives. Furthermore, particular agronomic traits such as fruit ripening, fragrance, and stress response are specifically selected for in the melon subspecies. These results represent distinctive footprints of selective breeding that shaped today’s melon. The sequences and genomic relations between land races, wild relatives, and cultivars will serve the community to identify genetic diversity, optimize experimental designs, and enhance crop development.

QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon recombinant inbred lines population supported byde novoassembly of their parental genomes

“…The substantial intra-chromosomal rearrangements spanning nearly half of chromosome 6 that differ between our parents also appears in the recently published de-novo assemblies of “Payzawat” and ‘Harukei-3′ genomes [ 51 , 52 ]. Previous SVs reported in melon, mainly attributed to transposable elements and some to meiotic crossovers [ 32 , 33 , 49 , 50 ], but these studies were focused on events of relatively small DNA fragments (<0.5 Mb). Examples for large-scale rearrangements have been reported in barley, including two frequent large inversions (>5 Mb) found in elite barley lines that are attributed to mutation breeding and the expansion of geographical range [ 70 ].…”

“…Out of the 1412 genes missing from either “Tam Dew” or “Dulce”, none were found within a QTL interval. Nonetheless, recent publications report on PAVs related to melon domestication in a region on chromosome 5 containing resistance genes, such as the protein coding Vat ( Virus aphid transmission ) [ 49 , 50 ]. Though “Tam Dew” and “Dulce” are both elite cultivars ( C. melo ssp.…”

“…A recent study has characterized in detail small to medium SVs (50 bp – 100Kb) and provided an important layer of information, e.g. annotated PAVs in resistance genes on chromosome 5 [ 50 ]. The genome assembly of “Payzawat” melon cultivar using long-read sequencing, detected large inversions across chromosome 6 when compared to the latest version of the melon reference genome [ 51 ].…”

Copy Number Variation among Resistance Genes Analogues in Brassica napus

“…Recently, several studies have reported CNV events across various crop species, including rice [ 27 , 36 ], wheat [ 85 ], barley [ 86 ], maize [ 52 , 87 ], soybean [ 46 ], melon [ 88 ] and cannabis [ 89 ]. Most of these studies have linked CNV analysis with agronomic traits.…”

A cryptic variation in a member of the Ovate Family Proteins is underlying the melon fruit shape QTL fsqs8.1

“…Domínguez et al ( 2020) found associations of transposon element insertion polymorphisms with major agronomic traits and secondary metabolites in cultivated tomato. Similarly, evidence of the role of retrotransposons on the evolution of the genome and modification of gene expression has also been reported in melon (Demirci et al 2021;Sanseverino et al 2015;Yano et al 2020). Thus, fsqs8.1 is perhaps another case of gene expression changes due to structural variation mediated by transposon activity.…”