Whole genome resequencing of four Italian sweet pepper landraces provides insights on sequence variation in genes of agronomic value

Abstract

Sweet pepper (Capsicum annuum L.) is a high value crop and one of the most widely grown vegetables belonging to the Solanaceae family. in addition to commercial varieties and f 1 hybrids, a multitude of landraces are grown, whose genetic combination is the result of hundreds of years of random, environmental, and farmer selection. High genetic diversity exists in the landrace gene pool which however has scarcely been studied, thus bounding their cultivation. We re-sequenced four pepper inbred lines, within as many italian landraces, which representative of as many fruit types: big sized blocky with sunken apex ('Quadrato') and protruding apex or heart shaped ('cuneo'), elongated ('corno') and smaller sized sub-spherical ('tumaticot'). each genomic sequence was obtained through Illumina platform at coverage ranging from 39 to 44×, and reconstructed at a chromosome scale. About 35.5k genes were predicted in each inbred line, of which 22,017 were shared among them and the reference genome (accession 'CM334'). Distinctive variations in miRNAs, resistance gene analogues (RGAs) and susceptibility genes (S-genes) were detected. A detailed survey of the Snp/indels occurring in genes affecting fruit size, shape and quality identified the highest frequencies of variation in regulatory regions. Many structural variations were identified as presence/absence variations (PAVs), notably in resistance gene analogues (RGAs) and in the capsanthin/capsorubin synthase (ccS) gene. the large allelic diversity observed in the four inbred lines suggests their potential use as a pre-breeding resource and represents a one-stop resource for C. annuum genomics and a key tool for dissecting the path from sequence variation to phenotype.

Whole-genome assembly of Corylus avellana cv “Tonda Gentile delle Langhe” using linked-reads (10X Genomics)

“…Unplaced scaffolds showed a lower rate of heterozygosity (0.60%). These data were expected due to the allogamous behavior of hazelnut and are comparable to those of other outbred species (∼1%; Velasco et al 2007 ; Acquadro et al 2017 ), and higher than the ones obtained in inbred species (∼0.1%; Barchi et al 2019 ; Acquadro et al 2020a ).…”

“…, Juglans microcarpa and J. regia , the most represented RGAs belong to RLK while few TNLs were identified ( Zhu et al 2019 ). Comparable results have been obtained in other non-woody species, like Solanaceae species such as Capsicum annuum , Solanum melongena , Solanum lycopersicum , and Solanum tuberosum ( Barchi et al 2019 ; Acquadro et al 2020a ). Furthermore, Kim et al (2012) highlighted that some Asterids contain functional TNLs, whereas others do not.…”

“…SNP/Indels were counted and analyzed using custom bash scripts. The estimation of the genome heterozygosity level was calculated by considering the ratio between the number of SNP/Indels (called in heterozygous state) and the size of the assembled genome after removal of Ns (404.097.498 bp) as previously reported ( Acquadro et al 2020a ).…”

Improved genome assembly and pan‐genome provide key insights into eggplant domestication and breeding

“…SNPs/indels were counted and analyzed using bcftools. The estimation of the heterozygous level of each genome (i.e., ‘genome level’) was calculated by considering, for each accession, the ratio between the number of SNPs/indels (called heterozygous state) and the ungapped size of the pan‐genome, deprived of Ns (1.17 Gb) as previously reported (Acquadro et al ., 2020 ). Vcftools (Danecek et al ., 2011 ) was applied to count the number of SNPs along the reference genome using a sliding window approach (1‐Mb windows, sliding in 500‐kb steps).…”

Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis

“…Deep sequencing technology has led to the identification of numerous miRNAs in plant genomes from species such as Italian sweet pepper [20], tea, mulberry, Chinese cabbage, turnip, longan (Dimocarpus longan Lour. ), bread wheat, Artemisia annua, Populus euphratica, Moringa oleifera, and Solanum lycopersicum [21][22][23][24][25][26][27][28][29][30].…”