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

2013 ◽  
Vol 93 (3) ◽  
pp. 435-444 ◽  
Author(s):  
Makiko Mimura
Keyword(s):  
Phenotypic Variation ◽  
Lotus Japonicus ◽  
Mantel Test ◽  
Total Biomass ◽  
Clinal Variation ◽  
Legume Species ◽  
Partial Mantel Test ◽  
Model Legume ◽  
Japanese Archipelago ◽  
The Japanese Archipelago

Mimura, M. 2013. Genetic and phenotypic variation in Lotus japonicus (Regel) K. Larsen, a model legume species. Can. J. Plant Sci. 93: 435–444. Lotus japonicus is a model legume species with more than 90% of its gene space determined; however, its ecological and evolutionary background is little known. The genetic and phenotypic variation of this model species was investigated within the Japanese Archipelago, where it exists in various climates and has experienced repeated vegetative shifts in conjunction with historical climate changes, using nuclear microsatellite loci and common garden experiments. The partial Mantel test was performed to detect the influence of phylogeographic effects on phenotypic variation among accessions along environmental gradients. Western Japan showed more complex genetic population structures than northern Japan, which may reflect past population dynamics. The total biomass demonstrated clinal variation with a climatic variable (ClimatePC). The trend was significant in a partial Mantel test when controlling for genetic distance, which is independent of the environmental distance. This suggests adaptive divergence within the Japanese Archipelago. With highly accessible genome information, L. japonicus appears to be a promising species for future ecological and evolutionary studies.

scholarly journals Root, Root Hair, and Symbiotic Mutants of the Model Legume Lotus japonicus

2002 ◽  
Vol 15 (1) ◽  
pp. 17-26 ◽  
Author(s):  
Masayoshi Kawaguchi ◽  
Haruko Imaizumi-Anraku ◽  
Hiroyuki Koiwa ◽  
Sinobu Niwa ◽  
Akira Ikuta ◽  
...  
Keyword(s):  
Root Hair ◽  
Phenotypic Variation ◽  
Developmental Process ◽  
Lotus Japonicus ◽  
Root Hairs ◽  
Model Legume ◽  
Nodule Number ◽  
Stable Mutant ◽  
Mutant Lines ◽  
Hypernodulating Mutants

To gain an overview of plant factors controlling nodule number and organogenesis, an extensive screening using model legume Lotus japonicus was carried out. This screening involved 40,000 M2 seeds, and 32 stable mutant lines were isolated. From these, 16 mutant lines maintaining the phenotypic variation were selected and genetically analyzed. With respect to nodule number, four loci were identified, Ljsym77, Ljsym78, slippery root (slp), and radial organization1 (rdo1). The former two mutants have an increased number of nodules, while the latter two have a decreased number. Ljsym78-1 and Ljsym78-2 are hypernodulating mutants with a branched root system and were found to be allelic to Ljsym16. The phenotype of the Ljsym77 mutant was highly pleiotropic, being deficient in light and gravity responses. The slp mutant was isolated as a low-nodulating mutant lacking root hairs. Concerning nodule organogenesis, nine symbiotic loci were identified, including the two loci alb1 and fen1. Mutants affecting the developmental process of nodule organogenesis were placed in three phenotypic categories: Nod¯ (Ljsym70 to Ljsym73), Hist¯ (alb1-1, alb1-2, and Ljsym79), and Fix¯ (fen1, Ljsym75, and Ljsym81).

LegumeDB1 bioinformatics resource: comparative genomic analysis and novel cross-genera marker identification in lupin and pasture legume species

Genome ◽  
2006 ◽  
Vol 49 (6) ◽  
pp. 689-699 ◽  
Author(s):  
P Moolhuijzen ◽  
M Cakir ◽  
A Hunter ◽  
D Schibeci ◽  
A Macgregor ◽  
...  
Keyword(s):  
Medicago Truncatula ◽  
Expressed Sequence Tags ◽  
Lotus Japonicus ◽  
Comparative Genomic ◽  
Legume Species ◽  
Model Legume ◽  
Bioinformatics Resource ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Pasture Legume

The identification of markers in legume pasture crops, which can be associated with traits such as protein and lipid production, disease resistance, and reduced pod shattering, is generally accepted as an important strategy for improving the agronomic performance of these crops. It has been demonstrated that many quantitative trait loci (QTLs) identified in one species can be found in other plant species. Detailed legume comparative genomic analyses can characterize the genome organization between model legume species (e.g., Medicago truncatula, Lotus japonicus) and economically important crops such as soybean (Glycine max), pea (Pisum sativum), chickpea (Cicer arietinum), and lupin (Lupinus angustifolius), thereby identifying candidate gene markers that can be used to track QTLs in lupin and pasture legume breeding. LegumeDB is a Web-based bioinformatics resource for legume researchers. LegumeDB analysis of Medicago truncatula expressed sequence tags (ESTs) has identified novel simple sequence repeat (SSR) markers (16 tested), some of which have been putatively linked to symbiosome membrane proteins in root nodules and cell-wall proteins important in plant-pathogen defence mechanisms. These novel markers by preliminary PCR assays have been detected in Medicago truncatula and detected in at least one other legume species, Lotus japonicus, Glycine max, Cicer arietinum, and (or) Lupinus angustifolius (15/16 tested). Ongoing research has validated some of these markers to map them in a range of legume species that can then be used to compile composite genetic and physical maps. In this paper, we outline the features and capabilities of LegumeDB as an interactive application that provides legume genetic and physical comparative maps, and the efficient feature identification and annotation of the vast tracks of model legume sequences for convenient data integration and visualization. LegumeDB has been used to identify potential novel cross-genera polymorphic legume markers that map to agronomic traits, supporting the accelerated identification of molecular genetic factors underpinning important agronomic attributes in lupin.Key words: legumes, comparative genomics, bioinformatics, expressed sequence tags (ESTs), simple sequence repeats (SSRs).

Origin and formation of Yaponesians based on genome sequences

Impact ◽  
2020 ◽  
Vol 2020 (7) ◽  
pp. 56-58
Author(s):  
Naruya Saitou
Keyword(s):  
Population Genetics ◽  
Human Migration ◽  
Human Populations ◽  
Genome Sequences ◽  
Japanese Archipelago ◽  
Broad Term ◽  
The Japanese Archipelago ◽  
Ebb And Flow ◽  
National Institute Of Genetics

The ebb and flow of human migration across the planet can nowadays be probed with advanced archaeology, linguistics, anthropology and genomics. Together, these can provide a convincing picture of the various divergences and convergences of different human populations across vast areas. It is now possible to better understand how, why and where a particular group or society arose. Professor Naruya Saitou of the Population Genetics Laboratory at the National Institute of Genetics in Mishima has dedicated his career to the synthesis of these disciplines. The current focus of his research is on understanding the origins and formation of the Yaponesian people. This broad term was coined by writer Toshio Shimao in 1960s to encompass the diverse peoples of the Japanese Archipelago over its many thousands of years of inhabitation. Saitou's research is helping to uncover Japan's ancient past.

Geographical variation in the cranial and external characters of the little tube-nosed bat,Murina silvatica in the Japanese archipelago

2005 ◽  
Vol 50 (3) ◽  
pp. 309-322 ◽  
Author(s):  
Dai Fukui ◽  
Kishio Maeda ◽  
David A. Hill ◽  
Sumiko Matsumura ◽  
Naoki Agetsuma
Keyword(s):  
Geographical Variation ◽  
Japanese Archipelago ◽  
The Japanese Archipelago

Morphometric studies of polyploid Cardamine species (Brassicaceae) from Japan: solving a long-standing taxonomic and nomenclatural controversy

2010 ◽  
Vol 23 (2) ◽  
pp. 94 ◽  
Author(s):  
Judita Lihová ◽  
Hiroshi Kudoh ◽  
Karol Marhold
Keyword(s):  
Ploidy Level ◽  
Morphological Variation ◽  
East Asian ◽  
Species Boundaries ◽  
Morphometric Data ◽  
Evolutionary Mechanism ◽  
Taxonomic Treatment ◽  
Japanese Archipelago ◽  
Level Data ◽  
The Japanese Archipelago

Polyploidy is an important evolutionary mechanism and speciation mode in plants; however, delimitation of species boundaries in polyploid complexes is often a difficult task. In the present paper, we explore morphological variation in a group of East Asian Cardamine polyploids that have long been shrouded in taxonomic and nomenclatural confusion. We relate the present morphometric data of 41 sampled populations with recently published ploidy-level data, and propose a revised taxonomic treatment, including the designation of several lectotypes. The following species are recognised in Japan: C. schinziana O.E.Schulz (2n = 6x, 8x), C. torrentis Nakai (2n = 8x), C. valida (Takeda) Nakai (2n = 4x) and C. yezoensis Maxim. (2n = 6x−12x). C. amariformis Nakai (2n = 4x) from Korea is also discussed, although it may be conspecific with C. valida, pending further studies. Distribution of these taxa in the Japanese Archipelago is characterised, including comments on their occurrence outside of Japan.

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