CREA Research Centre for Cereal and Industrial Crops, S.S. 673, km 25.200, 71122, Foggia, Italy.
Sequentia Biotech SL, Carrer d'Àlaba, 61, Barcelona, Spain.
BMC Genom Data. 2022 Mar 25;23(1):21. doi: 10.1186/s12863-022-01039-9.
Pepper is a major crop species of the Solanaceae family, largely appreciated for its high nutritional and healthy contribution to human diets. In the Mediterranean basin, the favorable pedoclimatic conditions enhanced the selection of several diversified landraces cultivated pepper (Capsicum annuum), for whom Italy can be considered a main pole of diversification. Hence, a survey of traditional C. annuum genetic resources is essential for deep understanding of such diversity and for applications in genomics assisted breeding. Here, we report whole-genome resequencing analyses of two sweet and two pungent genotypes highly diffused in South Italy and representative of the variability for shape, colour and nutritional properties.
The four genomes were reconstructed at a chromosomal scale using a reference-guided approach, based on a dataset of 2.6 billion paired-end reads, corresponding to 20× genome coverage and a mapping rate above 99% for a final genomes size of approximately 3 Gb. After five iterations of variant calling, a total of 29,258,818 single nucleotide polymorphisms (SNPs) and 1,879,112 InDels, were identified. Substantial differences were observed among the four genomes based on geographical origin, with chromosomes 9 and 11 showing more polymorphisms in the accessions with higher fruit weight and absence of pungency. Among the identified variants, a small private indel (T - > TA) shared between sweet and big fruits accessions induces a frameshift with the generation of a new stop codon in a gene annotated as extensin, whereas two private SNPs within hot types were identified in 1-aminocyclopropane-1-carboxylate oxidase (ACO), a key gene involved in fruit ripening. The estimation of repetitive elements highlights a preponderant presence of Long Terminal Repeats (LTRs), the majority of which belonged to Gypsy superfamily. By comparing the four genomes with publicly available references including 'CM334' and Zunla-1 highlight the presence of 49,475 shared gene families.
The new genomic sequences aim to enrich the whole genome information of pepper local varieties, providing a valuable tool for precision gene mapping, marker discovery, comparative studies. Such knowledge widens the frontiers to understand the selection history of Italian pepper landraces toward the recognition of specificity local agri-food products marks.
辣椒是茄科的主要作物之一，因其对人类饮食的高营养价值和健康贡献而受到广泛关注。在地中海盆地，有利的土壤气候条件促进了多种多样化的地方辣椒（Capsicum annuum）品种的选择，意大利可以被视为多样化的主要极点。因此，对传统 C. annuum 遗传资源进行调查对于深入了解这种多样性以及在基因组辅助育种中的应用至关重要。在这里，我们报告了对两个在意大利南部广泛传播的甜椒和两个辣椒基因型的全基因组重测序分析，这些基因型代表了形状、颜色和营养特性的可变性。
使用基于参考的方法，基于 26 亿对末端读取的数据集，对四个基因组进行了染色体规模的重建，对应于 20 倍的基因组覆盖度和超过 99%的映射率，最终基因组大小约为 30 亿。经过五次变异调用迭代，共鉴定出 29258818 个单核苷酸多态性（SNP）和 1879112 个插入缺失。根据地理位置，四个基因组之间存在明显差异，果实重量较高且不辣的品种的染色体 9 和 11 显示出更多的多态性。在所鉴定的变体中，甜椒和大果品种之间共享的一个小的私有插入缺失（T - > TA）导致一个外显子的移码，并在一个被注释为伸展蛋白的基因中产生一个新的终止密码子，而在热型中鉴定出的两个私有 SNP 则存在于 1-氨基环丙烷-1-羧酸氧化酶（ACO）中，这是一个与果实成熟有关的关键基因。重复元件的估计强调了长末端重复（LTRs）的优势存在，其中大多数属于 Gypsy 超家族。通过将四个基因组与包括'CM334'和 Zunla-1 在内的公开参考基因组进行比较，突出了 49475 个共享基因家族的存在。
新的基因组序列旨在丰富当地辣椒品种的全基因组信息，为基因精确定位、标记发现、比较研究提供了有价值的工具。这些知识拓宽了我们的视野，有助于了解意大利地方辣椒品种的选择历史，以识别特定的地方农产品标志。
