Genomic Analyses Yield Markers for Identifying Agronomically Important Genes in Potato

Abstract

Wild potato species have substantial phenotypic and physiological diversity. Here, we report a comprehensive assessment of wild and cultivated potato species based on genomic analyses of 201 accessions of Solanum section Petota. We sequenced the genomes of these 201 accessions and identified 6 487 006 high-quality single nucleotide polymorphisms (SNPs) from 167 accessions in clade 4 of Solanum section Petota, including 146 wild and 21 cultivated diploid potato accessions with a broad geographic distribution. Genome-wide genetic variation analysis showed that the diversity of wild potatoes is higher than that of cultivated potatoes, and much higher genetic diversity in the agronomically important disease resistance genes was observed in wild potatoes. Furthermore, by exploiting information about known quantitative trait loci (QTL), we identified 609 genes under selection, including those correlated with the loss of bitterness in tubers and those involved in tuberization, two major domesticated traits of potato. Phylogenetic analyses revealed a north-south division of all species in clade 4, not just those in the S. brevicaule complex, and further supported S. candolleanum as the progenitor of cultivated potato and the monophyletic origin of cultivated potato in southern Peru. In addition, we analyzed the genome of S. candolleanum and identified 529 genes lost in cultivated potato. Collectively, the molecular markers generated in this study provide a valuable resource for the identification of agronomically important genes useful for potato breeding.

Potato Germplasm Enhancement Enters the Genomics Era

“…The authors suggested that, in these crops, germplasm resources are accessible and have received considerable attention from breeders. A recent genomics study revealed a high level of genetic diversity for disease resistance traits in wild potato species [28]. Thus, the case for continued use of germplasm enhancement to improve disease resistance seems strong.…”

“…A large sequencing effort on 84 tomato genomes has recently revealed extensive species-and accession-specific polymorphisms [110]. Similarly, genomic analysis of 201 wild and cultivated potato accessions revealed high levels of diversity, especially in wild populations, and over 600 genes associated with domestication traits [28]. As genome annotation information grows, scientists will be able to identify SNPs in or near genes of interest and predict whether they are likely to result in a functionally different protein product [106].…”

Analysis and selection of parental forms for crossbreeding of early potatoes for the arid conditions of the Middle Volga region

“…In potato breeding, hybridization is the main method of creating new populations/forms for selection. The pedigree of modern potato varieties shows that they are obtained by selection from hybrid populations, individual valuable traits, or their combinations, which are absent from the cultural species S. tuberosum (immunity to viruses, late blight, nematode) [8,9].…”

An Integrated Approach to Creating Scab-Resistant Apple: Phytopathological Testing and Marker-Assisted Selection

“…Формирование биосинтетических путей накопления алкалоидов у растений семейства пасленовых происходило в результате дупликаций генов, кодирующих ферменты первичного метаболизма, приводящих к неофункционализации гена, либо вовлечением ферментов первичного метаболизма во вторичный (субфункционализация) и последующей организацией кластеров (Ober, 2005). В последние годы секвенированы геномы дикого картофеля (Li et al, 2018), петунии (Bombarely et al, 2016), перца (Qin et al, 2014), витании (Knoch et al, 2018) с аннотированием генов, реализующих вторичный метаболизм (Aversano et al, 2015;Xu et al, 2017). Геномные данные позволяют проводить филогенетический анализ генов вторичного метаболизма и выявлять события дупликации генов и последующей нео-либо суб-функционализации, либо псевдогенизации и потери функций (D'Amelia et al, 2018;Nagy et al, 2005;Zhang et al, 2015).…”