Proc. Natl. Acad. Sci. USA Vol. 96, pp. 8265–8270, July 1999 Plant Biology High gene density is conserved at syntenic loci of small and large grass genomes CATHERINE FEUILLET AND BEAT KELLER* Institute of Plant Biology, University of Zu¨rich, Zollikerstrasse 107, CH-8008 Zu¨rich, Switzerland Communicated by Ronald L. Phillips, University of Minnesota, St. Paul, MN, April 26, 1999 (received for review December 3, 1998) ABSTRACT Comparative genomic analysis at the genetic- DNA (7). These studies suggested that the discrepancy in the map level has shown extensive conservation of the gene order size of the intergenic regions in different grasses correlated between the different grass genomes in many chromosomal with the accumulation of repeated elements between the genes regions. However, little is known about the gene organization in large genome species. Very little data are available on the in grass genomes at the microlevel. Comparison of gene- gene distribution in large and complex genomes of barley and coding regions between maize, rice, and sorghum showed that wheat. In barley, a gene density of one gene every 20 kb was the distance between the genes is correlated with the genome found in the region surrounding the mlo gene (8). In wheat, size. We have investigated the microcolinearity at Lrk gene loci Gill et al. (9) demonstrated by deletion mapping that the genes in the genomes of four grass species: wheat, barley, maize, and are distributed nonrandomly in gene-rich regions at the distal rice. The Lrk genes, which encode receptor-like kinases, were end of chromosome group 1. Recently, the analysis of a found to be consistently associated with another type of genomic fragment at a starch-branching enzyme I locus on receptor-like kinase (Tak) on chromosome groups 1 and 3 in chromosome 7D in Triticum tauschii (10) showed the presence Triticeae and on chromosomes homoeologous to Triticeae of three tandemly repeated genes within 16 kb. group 3 in the other grass genomes. On Triticeae chromosome Here, we isolated and compared genomic fragments up to 23 group 1, Tak and Lrk together with genes putatively encoding kb in size surrounding the receptor-like kinase gene Lrk10 (11) NBS͞LRR proteins form a cluster of genes possibly involved on Triticeae homoeologous chromosome groups 1 and 3 in in signal transduction. Comparison of the gene composition at wheat, barley, maize, and rice. Comparison of the gene com- orthologous Lrk loci in wheat, barley, and rice revealed a position and organization at both chromosomal locations maximal gene density of one gene per 4–5 kb, very similar to revealed at the microlevel the presence of gene-rich regions in the gene density in Arabidopsis thaliana. We conclude that the different grass genomes and indicated the emergence of small and large grass genomes contain regions that are highly different receptor-like kinase gene families during evolution. enriched in genes with very little or no repetitive DNA. The The finding of high-gene-density regions independent of the comparison of the gene organization suggested various ge- genome size is of importance for map-based cloning in large nome rearrangements during the evolution of the different genomes. grass species. MATERIALS AND METHODS The extensive contiguous genomic sequencing of the dicot model species Arabidopsis thaliana (1) has shown that the gene ␭ and Yeast Artificial Chromosome (YAC) Library Screen- density is of about one gene every 4–5 kb (2). However, A. ing. Genomic libraries from wheat (Triticum aestivum, var. thaliana has a small genome and low amount of repetitive DNA ThatcherLr10) and barley (Hordeum vulgare, var. Igri) (Strat- compared with other plant species with more complex ge- agene) were screened with the 32P-labeled pLrk10-A wheat nomes. Grass genomes are highly variable in size, ranging from probe (12) under high (65°C) stringency. The barley genomic diploid species with 415 Mb in rice to 16,000 Mb in the library was also screened under high stringency with a 32P- hexaploid wheat. The accumulation of repetitive sequences, labeled 610-bp HindIII͞EcoRV fragment of the wheat clone which can represent up to 80%, such as in wheat (3), raises the 3ASLrk. Genomic libraries from rice (Oryza sativa, var. IR36) question of the gene distribution in these complex genomes. and maize (Zea mays, var. B73) (CLONTECH) were screened Comparative mapping studies have established syntenic rela- with the 32P-labeled pLrk10-A probe under low (50°C) strin- tionships between the different chromosome groups in the gency. A barley (H. vulgare, var. Franka) YAC library grass genomes (4). Most of these studies have been performed (MALTAGEN) was screened by PCR by using primers (5Ј- at the genetic map level, and little is known about the GGAAGTTAGCATGCTCGG-3Ј and 5Ј-CATACCGCCAG- consequences of the evolutionary divergence on the gene GCATACAG-3Ј) designed in conserved sequences of the composition and organization at the molecular level. Recent extracellular domain of the Hv1Lrk1 and Hv1Lrk2 genes. The analysis of large, orthologous genomic fragments from maize, YAC sublibrary was constructed in ␭ZAPII (Stratagene) rice, and sorghum genomes demonstrated that the gene density according to Whittaker and Rakesh (13). The library was varies in correlation with the genome size. Indeed, at the screened with the 32P-labeled probe pLrk10-A as well as probes Sh2͞A1 region, the intergenic regions were about 7 times corresponding to the nucleotide-binding site (NBS) regions of longer in maize compared with the orthologous regions in rice HV1LRR1 and HV1LRR2. The NBS region of HV1LRR1 was and sorghum (5). At the Adh1͞u22 locus, the genes were obtained by PCR amplification on Hv1Lrr1 (AF108008) with separated by more than 120 kb in maize, whereas the ortholo- the primers 5Ј-CACTCTTGTTGATCATGTGT-3Ј and 5Ј- gous genes in sorghum were only 50 kb apart (6). Molecular analysis of 280 kb at the maize Adh1 locus demonstrated the Abbreviations: NBS, nucleotide-binding site; LRR, leucine-rich re- presence of 10 retroelement families representing 60% of the peats; YAC, yeast artificial chromosome. Data deposition: The sequences reported in this paper have been The publication costs of this article were defrayed in part by page charge deposited in the GenBank database (accession nos. U76215, U78762, AF085164–AF085169, AF100764–AF100771, and AF108008– payment. This article must therefore be hereby marked ‘‘advertisement’’ in AF108015). accordance with 18 U.S.C. §1734 solely to indicate this fact. *To whom reprint requests should be addressed. e-mail: bkeller@ PNAS is available online at www.pnas.org. botinst.unizh.ch. 8265 Downloaded by guest on September 25, 2021 8266 Plant Biology: Feuillet and Keller Proc. Natl. Acad. Sci. USA 96 (1999) AAGCTGACCTTTAGGATC-3Ј. The NBS region of nucleotide sequence level with RPM1, a resistance gene from HV1LRR2 consisted of a EcoRI͞NotI fragment of 1.4 kb A. thaliana against a bacterial disease (15). RPM1 belongs to isolated from Hv1Lrr2 (AF108010). the resistance gene class encoding intracellular NBS͞LRR Sequence Analysis. Sequencing reactions were performed types of proteins. However, ␺Lrr10 (U76215) is probably a with the Thermo Sequenase cycle sequencing kit (Amersham) pseudogene because the coding sequence for the first 70 aa at according to the instructions of the manufacturer and subse- the N-terminal sequence is lacking compared with RPM1.In quently were run on an automatic DNA sequencer. The addition, there is a frameshift mutation at position 943 and an sequences were analyzed with GCG software (Wisconsin in-frame stop codon at position 1327. Thus, within 14 kb, at the Package), BCM GENEFINDER software, and the BLAST program locus encoding the leaf rust-resistance gene Lr10 (11) on of the National Center for Biotechnology Information (http:͞͞ chromosome 1AS, there are two genes encoding receptor-like www.ncbi.nlm.nih.gov͞). kinases and one pseudogene homologous to resistance genes. Genetic Mapping. Linkage analysis in wheat and barley was To compare the conservation of gene organization between performed as described previously (14). Mapping in maize was the Triticeae genomes, we isolated the corresponding region performed on 56 F2 plants from a cross between the inbred from barley. Under high stringency, the extracellular domain lines Tx303 and CO159 at the University of Missouri– of Lrk10 (pLrk10-A) hybridized with two unique XbaI frag- Columbia. ments that cosegregated on barley chromosome 1HS (14). We screened a barley genomic library and isolated fragments RESULTS corresponding to the two loci (XHv1.1 and XHv1.2) detected by Southern hybridization (Fig. 1b). DNA stretches of 23 and A Cluster of Receptor-Like Kinase Genes Is Located in a 5 kb were sequenced at the XHv1.1 and XHv1.2 loci, respec- Gene-Rich Region on Wheat and Barley Chromosome Group tively. At the XHv1.1 locus, we detected two genes, Hv1Lrk1 1. To investigate the gene density and gene organization at the and Hv1Tak1, homologous to Lrk10 and Tak10, respectively. Lrk10 locus (11) in wheat, a genomic fragment of 13,887 bp Similarly, two genes, Hv1Lrk2 and Hv1Tak2, were found at the (␭W1AS) containing the Lrk10 gene was isolated and char- XHv1.2 locus (Fig. 1b). The relative orientation of the Hv1Lrk acterized. Two additional genes were found upstream from and Hv1Tak genes was identical to the gene organization found Lrk10 (Fig. 1a). At a 620-bp distance from the Lrk10 transla- on wheat chromosome 1AS (Fig. 1a), i.e., Hv1Lrk and Hv1Tak tion start site, a second gene encoding another receptor-like genes were found in opposite orientation (Fig. 1b). Compar- kinase (Tak10, U78762) starts in reverse orientation. The ison of both barley Hv1LRK1͞Hv1LRK2 and Hv1TAK1͞ TAK10 protein showed high homology (68%) to LRK10 in the Hv1TAK2 proteins with the wheat LRK10 and TAK10, re- Ser͞Thr kinase domain. In addition, the Tak10 gene contains spectively, showed up to 79% homology at the amino acid level.