Analysis of genetic diversity and morphological traits of Japanese Lotus japonicus for establishment of a core collection

Abstract

Lotus japonicus is a model legume used by researchers worldwide to study nodulation and other aspects of legume biology. We investigated 15 morphological traits in a large collection of wild L. japonicus accessions collected in Japan, and also analyzed the genetic diversity among them, in order to develop a core collection based on genome-wide SSR polymorphisms. We found a wide diversity of morphological traits among the accessions. A total of 321 putative alleles were detected using 25 SSR primer pairs. The average observed and expected heterozygosity scores for individual loci were 0.014 and 0.772, respectively, indicating a high degree of homozygosity. The accessions were divided into 9 clusters based on G ST ' and STRUCTURE analyses. In addition, we selected 20 accessions to serve as the representative core collection based on SSR analysis. The range of morphological traits in the core collection was representative of that found in the entire collection. This core collection will be useful for genome-wide studies and data obtained for this model species should lead to numerous practical applications for crop legumes. All accessions from the entire collection are available from Legume Base (http://www.legumebase.brc.miyazaki-u.ac.jp/), a section of the National BioResource Project in Japan.

The Lotus japonicus Genome

“…So far, around 30 L. japonicus ecotypes and related species such as Lotus burttii have been re-sequenced providing single nucleotide polymorphisms and thereby setting the stage for genome-wide association studies accessing natural variation and biodiversity (Kai et al 2010; Andersen and Sato, pers.com). The L. japonicus genespace has been sequenced and re-sequenced in different ecotypes and Lotus species to uncover the biodiversity, and a well-annotated genome has been established as a basis for comparative genome analysis within the genus and the legume family.…”

“…22.1). Recently, Kai et al (2010) selected 20 accessions to serve as a representative core collection based on simple sequence repeats (SSR) polymorphisms and morphological traits (Fig. At present, 180 accessions are stocked and 108 accessions are available via "LegumeBase" (Table 22.1).…”

“…"LegumeBase" contains an interactive database for selecting LjMG RILs based on the 13 phenotypic traits evaluated by . 22.2 Population structures estimated by STRUC-TURE analysis at K = 9 using data for 25 nuclear genetic loci (Kai et al 2010). In addition, two other kinds of RILs were deposited from Aarhus University, Denmark.…”

The National BioResource Project (NBRP) Lotus and Glycine in Japan

“…Recently, Kai et al (2010) selected 20 accessions to serve as a representative core collection based on SSR (Simple Sequence Repeats) polymorphisms (Table 1). The range of morphological traits in the core collection was representative of that found in the entire collection.…”

Genetic and phenotypic variation inLotus japonicus(Regel) K. Larsen, a model legume species

“…Besides studies on its symbiotic nitrogen fixation, the species may also contribute to an understanding of adaptive ecology and evolution across heterogeneous environments. Although it has been reported that L. japonicus has significant trait variation within species (Kai et al 2010), little research has been initiated with regard to the essential ecological basis for the species, such as the historical range dynamics, geographic and genetic structure, seed/pollen dispersal, and phenotypic variations [but see Suginobu et al (1988) for trait evaluations]. Natural populations that are the subject of ecological and evolutionary studies are prone to local environmental pressures, and to numerous historical events including isolation and migration, which often lead to genetically and phenotypically divergent populations without natural selection.…”