Estimating genome conservation between crop and model legume species

Hong Choi

Jeong Mun

Dong Kim

Hongyan Zhu

Jeff Doyle+3 authors

^{Department of Plant Pathology and}^{College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616;}^{Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108;}^{Advanced Center for Genome Technology, University of Oklahoma, Norman, OK 73019;}^{John Innes Centre, Norwich NR4 7UH, United Kingdom;}^{Department of Plant Biology, Cornell University, Ithaca, NY 14853; and}^{Biological Research Center, Institute of Genetics, H-6701 Szeged, Hungary}

^{To whom correspondence should be addressed. E-mail:}ude.sivadcu@koocrd.

^{H.-K.C., J.-H.M., and D.-J.K. contributed equally to this work.}

Edited by Susan R. Wessler, University of Georgia, Athens, GA

Received 2004 Mar 30; Accepted 2004 Aug 13.

Abstract

Legumes are simultaneously one of the largest families of crop plants and a cornerstone in the biological nitrogen cycle. We combined molecular and phylogenetic analyses to evaluate genome conservation both within and between the two major clades of crop legumes. Genetic mapping of orthologous genes identifies broad conservation of genome macrostructure, especially within the galegoid legumes, while also highlighting inferred chromosomal rearrangements that may underlie the variation in chromosome number between these species. As a complement to comparative genetic mapping, we compared sequenced regions of the model legume Medicago truncatula with those of the diploid Lotus japonicus and the polyploid Glycine max. High conservation was observed between the genomes of M. truncatula and L. japonicus, whereas lower levels of conservation were evident between M. truncatula and G. max. In all cases, conserved genome microstructure was punctuated by significant structural divergence, including frequent insertion/deletion of individual genes or groups of genes and lineage-specific expansion/contraction of gene families. These results suggest that comparative mapping may have considerable utility for basic and applied research in the legumes, although its predictive value is likely to be tempered by phylogenetic distance and genome duplication.

Abstract

The Fabaceae, or legumes, are cultivated on 180 million hectares, involving ≈12% of Earth's arable land and accounting for ≈27% of the world's primary crop production (1). Their unusual capacity for symbiotic nitrogen fixation underlies their importance as a source of protein in the human diet and of nitrogen in both natural and agricultural ecosystems. Legumes are also increasingly recognized as a source of valuable secondary metabolites. These factors have fueled a significant increase in legume research over the past decade.

The ≈20,000 legume species are divided into three subfamilies: Mimosoideae, Caesalpinioideae, and the numerically and economically dominant Papilionoideae (2). With the notable exception of peanut, the important crop legumes occur in two Papilionoid clades, referred to here as the “phaseoloid” and “galegoid” legumes (Table 1). Despite their close phylogenetic affiliations (Fig. 1), the genetic systems represented within this group are diverse, ranging from simple autogamous diploids to complex out-crossing polyploids. Genome size also varies widely among legumes, with pea having a genome size 10 times that of some related diploid genera.

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Fig. 1.

Taxonomic relationships within the two major clades of crop legumes, the prevailing view of phylogeny for the species under analysis, with divergence times estimated based on Penalised Likelihood analysis (2). Most crop legumes occur either within the galegoid clade, including tribes Viceae, Trifolieae, and Cicereae, or within the phaseoloid clade, which is synonymous with the tribe Phaseoleae. MYA, million years ago.

Table 1.

Attributes of species used for synteny analysis

Species	Common name	Genome size, Mbp	N	Tribe	Clade	SL	PL	Genotypes
M. truncatula	Barrel medic	500	8	Trifoleae	Galegoid	183	130	A17, A20, DZA
M. sativa	Alfalfa	1,600	16	Trifoleae	Galegoid	70	68	Mscw2, Msq93
Pi. sativum	Pea	5,000	7	Viceae	Galegoid	101	68	JI15, JI281, JI399, JI194
G. max	Soybean	1,100	20	Phaseoleae	Phaseoloid	56	15	PI209322, Evans
V. radiata	Mung bean	520	11	Phaseoleae	Phaseoloid	62	31	TC1966, VC3890
Ph. vulgaris	Common bean	620	11	Phaseoleae	Phaseoloid	37	22	BAT93, Jalo
L. japonicus	Bird's foot trefoil	500	6	Loteae		67	44	Lotus filicaulis, L. japonicus Gifu

SL, sequenced loci; PL, polymorphic loci; N, gametic chromosome number.

The large number of important legume species precludes their simultaneous in-depth characterization. Moreover, several crop legumes have one or more characters (e.g., medium to large genomes and/or polyploid nature) that limit their utility as experimental systems. Two legumes with favorable genetic attributes, namely Medicago truncatula and Lotus japonicus, have been selected as model species and are the focus of large multinational genome projects. The early fruits of working with these well characterized genomes are evident in the recent advances in our understanding of symbiotic nitrogen fixation in both M. truncatula and L. japonicus (3).

A pressing need in legume genomics is to integrate knowledge gained from the study of model legume genomes with the biological and agronomic questions of importance in the crop species. Comparative genetic mapping is well established in several plant families, most notably the Poaceae (4), where initial studies predicted that synteny would greatly facilitate gene discovery among related species (5, 6). However, even closely related grass species (7, 8), in some cases members of the same species (9), can exhibit significant divergence in genome organization. It is important to know whether similar features are prevalent in other plant families, in particular because the extent of such differences may define the limits of comparative structural genomics as a strategy for applied agriculture.

Here we combined genetic and phylogenetic analyses to map putatively orthologous genes across seven legume species. Complementing the genetic linkage analysis, we surveyed the conservation of genome microstructure between M. truncatula and L. japonicus and M. truncatula and Glycine max (soybean) by comparing fully sequenced bacterial artificial chromosome (BAC) clones. The combined genetic, phylogenetic, and genomic analyses demonstrate extensive conservation of gene order and orthology between the crop and model legumes and also identify features of structural divergence between these genomes.

SL, sequenced loci; PL, polymorphic loci; N, gametic chromosome number.

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Acknowledgments

This work was supported by National Science Foundation Grant 0110206 (to D.R.C., N.D.Y., and D.-J.K.); the Samuel Roberts Noble Foundation (to B.R.); the European Union MEDICAGO project (QLG2-CT-2000-30676) and the Biotechnology and Biological Sciences Research Council (to N.E.); and Nemzeti Kutatás es Feilesztesi Program and the (HNDRP) [Országos Tudományos Kutatási Alap Programok (OTKA) and T038211, to G.B.K.].

Acknowledgments

Notes

This paper was submitted directly (Track II) to the PNAS office.

Abbreviations: BAC, bacterial artificial chromosome; NCBI, National Center for Biotechnology Information.

Notes

This paper was submitted directly (Track II) to the PNAS office.

Abbreviations: BAC, bacterial artificial chromosome; NCBI, National Center for Biotechnology Information.

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