Population genetic structure and classification of cultivated and wild pea (Pisum sp.) based on morphological traits and SSR markers

Abstract

Pea (Pisum sativum L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (Pisum sp.) remain controversial. To characterize patterns of genetic and morphological variation and investigate the classification of Pisum, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea, representing three species of Pisum and utilizing 34 morphological traits and 87 polymorphic simple sequence repeat markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of Pisum fulvum, Pisum abyssinicum, and some wild P. sativum accessions, whereas Groups II and III consisted of the two genetic groups under P. sativum that represented different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of Pisum, P. fulvum and P. abyssinicum possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of P. sativum described by some authors were not supported in this study, with the exception of several genotypes of P. sativum subsp. elatius that clustered with P. fulvum and P. abyssinicum. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.

Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics

“…Despite numerous studies focused on the classification of Pisum, this long-standing issue remains unresolved, and much confusion about pea domestication persists [49][50][51][52][53] . One point of contention is the taxonomic status of P. abyssinicum, namely, whether to regard it as an independent species or subspecies within P. sativum 54 .…”

“…Five seeds of 76 accessions representing different taxa of Pisum 50 were planted in glasshouse under natural conditions of the Institute of Crop Sciences, CAAS, Beijing in 2020. Fresh leaves of one plant for each accession were harvested to extract genomic DNA and resequenced using Illumina NovaSeq 6000 sequencing platform (Illumina).…”

Morpho-molecular genetic diversity and population structure analysis in garden pea (Pisum sativum L.) genotypes using simple sequence repeat markers

“…The results of the study indicated that the high proportion (94%) of variation was due to differences within population, while 6% was due to differences among the population. Liu et al [54] also reported the use of AMOVA in the genetic diversity study of garden pea and observed 68.14% variation within groups and species while there was 18.33% variation among species and 13.53% variation among groups within species. PCoA is one of the multivariate approaches for grouping of the genotypes based on similarity coefficients which provide more important information about major groups in comparison to the cluster analysis.…”

Genetic diversity and population structure analysis of a diverse panel of pea (Pisum sativum)

“…Pea (P. sativum L.) is a diploid (2n = 2x = 14) legume that belongs to species of Fabaceae, subfamily Papillionaceae, and the tribe Vicieae with a genome size of about 4,500 Mb (Jain et al, 2014;Yang et al, 2022;Rispail et al, 2023). Despite the pea's historical significance in genetics dating back to Mendel's pioneering work, genomic resources have only recently undergone notable improvements due to the release of the whole-genome sequence Kreplak et al (2019) and subsequent development of a reference genome and a pan-genome (Yang et al, 2022). These resources have provided valuable insights into the genetic makeup of the pea, facilitating more comprehensive genetic screenings and evaluations.…”