Legume Anchor Markers Link Syntenic Regions between Phaseolus Vulgaris, Lotus Japonicus, Medicago Truncatula and Arachis
Hougaard, Birgit Kristine, Madsen, Lene Heegaard, Sandal, Niels, de Carvalho Moretzsohn, Marcio, Fredslund, Jakob, Schauser, Leif, Nielsen, Anna Marie, Rohde, Trine, Sato, Shusei, Tabata, Satoshi, Bertioli, David John, Stougaard, Jens, Genetics
We have previously described a bioinformatics pipeline identifying comparative anchor-tagged sequence (CATS) loci, combined with design of intron-spanning primers. The derived anchor markers defining the linkage position of homologous genes are essential for evaluating genome conservation among related species and facilitate transfer of genetic and genome information between species. Here we validate this global approach in the common bean and in the AA genome complement of the allotetraploid peanut. We present the successful conversion of ~50% of the bioinformatics-defined primers into legume anchor markers in bean and diploid Arachis species. One hundred and four new loci representing single-copy genes were added to the existing bean map. These new legume anchor-marker loci enabled the alignment of genetic linkage maps through corresponding genes and provided an estimate of the extent of synteny and collinearity. Extensive macrosynteny between Lotus and bean was uncovered on 8 of the 11 bean chromosomes and large blocks of macrosynteny were also found between bean and Medicago. This suggests that anchor markers can facilitate a better understanding of the genes and genetics of important traits in crops with largely uncharacterized genomes using genetic and genome information from related model plants.
THE legume family (Leguminosae) is the third largest family of higher plants and includes >19,000 species (Lewis et al. 2005). Plants belonging to the family are diverse, and trees, shrubby perennials, annual herbs, ornamentals as well as agriculturally important crops are represented. Legumes play a critical role in natural ecosystems, agriculture, and agroforestry, where their ability to establish symbiosis with nitrogen-fixing rhizobial bacteria makes them efficient colonizers of low-nitrogen environments and desirable protein crops. Phaseolus vulgaris L. (common bean) is a particularly important source of protein. It serves as a staple food known as the poor man's meat and contains dietary fiber, minerals, vitamins, and various health promoting compounds (Guillon and Champ 2002; Leterme 2002). Arachis hypogaea (cultivated peanut) is in addition to being consumed in many human foods, the fifth most important oil crop and also a rich source of dietary protein for the chicken and pork industries (Graham and Vance 2003).
The legume family is divided into three subfamilies: Caesalpinioideae, Mimosoideae, and Papilionoideae. Most of the economically important legumes are members of the monophyletic subfamily Papilionoideae, which can be divided into four major clades. Although the legumes included in our study, Lotus japonicus, Medicago truncatula, bean, and Arachis are all in the Papilionoideae subfamily, they belong to three different clades: halogalegina, phaseoloid/millettioid, and aeschynomenoid/ dalbergioid. Lotus and Medicago are equally closely related to the bean and equally distantly related to Arachis (Doyle and Luckow 2003). Also the agronomical and genome characteristics of the legumes in our study differ. Both of the model legumes are herbaceous plants of limited agricultural use with relatively small genomes of ~470 Mb, while the common bean and cultivated peanut are major grain legumes with larger genomes of 588 Mbp and 2813 Mbp, respectively (http://data.kew.org/cvalues/homepage.html). In the bean there are >29,000 domesticated and 1300 wild accessions in germplasm banks (Broughton et al. 2003). However, the genetic base of the commercial cultivars of specific market classes is narrow. Less than 5% of the genetic diversity available has been used globally despite nearly a century of organized bean improvement (Broughton et al. 2003). Several genetic maps representing different populations have been established on a backbone of RFLP markers (Vallejos et al. 1992; Nodari et al. 1993; Freyre et al. 1998).
The cultivated peanut is an allotetraploid with an AABB genome complement. …