Summary The nucleotide binding site (NBS) is a characteristic domain of many plant resistance gene products. An increasing number of NBS‐encoding sequences are being identified through gene cloning, PCR amplification with degenerate primers, and genome sequencing projects. The NBS domain was analyzed from 14 known plant resistance genes and more than 400 homologs, representing 26 genera of monocotyledonous, dicotyle‐donous and one coniferous species. Two distinct groups of diverse sequences were identified, indicating divergence during evolution and an ancient origin for these sequences. One group was comprised of sequences encoding an N‐terminal domain with Toll/Interleukin‐1 receptor homology (TIR), including the known resistance genes, N, M, L6, RPP1 and RPP5. Surprisingly, this group was entirely absent from monocot species in searches of both random genomic sequences and large collections of ESTs. A second group contained monocot and dicot sequences, including the known resistance genes, RPS2, RPM1, I2, Mi, Dm3, Pi‐B, Xa1, RPP8, RPS5 and Prf. Amino acid signatures in the conserved motifs comprising the NBS domain clearly distinguished these two groups. The Arabidopsis genome is estimated to contain approximately 200 genes that encode related NBS motifs; TIR sequences were more abundant and outnumber non‐TIR sequences threefold. The Arabidopsis NBS sequences currently in the databases are located in approximately 21 genomic clusters and 14 isolated loci. NBS‐encoding sequences may be more prevalent in rice. The wide distribution of these sequences in the plant kingdom and their prevalence in the Arabidopsis and rice genomes indicate that they are ancient, diverse and common in plants. Sequence inferences suggest that these genes encode a novel class of nucleotide‐binding proteins.

The nucleotide binding site (NBS) is a characteristic domain of many plant resistance gene products. An increasing number of NBS-encoding sequences are being identified through gene cloning, PCR amplification with degenerate primers, and genome sequencing projects. The NBS domain was analyzed from 14 known plant resistance genes and more than 400 homologs, representing 26 genera of monocotyledonous, dicotyle-donous and one coniferous species. Two distinct groups of diverse sequences were identified, indicating divergence during evolution and an ancient origin for these sequences. One group was comprised of sequences encoding an N-terminal domain with Toll/Interleukin-1 receptor homology (TIR), including the known resistance genes, N, M, L6, RPP1 and RPP5. Surprisingly, this group was entirely absent from monocot species in searches of both random genomic sequences and large collections of ESTs. A second group contained monocot and dicot sequences, including the known resistance genes, RPS2, RPM1, I2, Mi, Dm3, Pi-B, Xa1, RPP8, RPS5 and Prf. Amino acid signatures in the conserved motifs comprising the NBS domain clearly distinguished these two groups. The Arabidopsis genome is estimated to contain approximately 200 genes that encode related NBS motifs; TIR sequences were more abundant and outnumber non-TIR sequences threefold. The Arabidopsis NBS sequences currently in the databases are located in approximately 21 genomic clusters and 14 isolated loci. NBS-encoding sequences may be more prevalent in rice. The wide distribution of these sequences in the plant kingdom and their prevalence in the Arabidopsis and rice genomes indicate that they are ancient, diverse and common in plants. Sequence inferences suggest that these genes encode a novel class of nucleotide-binding proteins.

This study presents the development and mapping of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers in chickpea. The mapping population is based on an inter-specific cross between domesticated and non-domesticated genotypes of chickpea (Cicer arietinum ICC 4958 × C. reticulatum PI 489777). This same population has been the focus of previous studies, permitting integration of new and legacy genetic markers into a single genetic map. We report a set of 311 novel SSR markers (designated ICCM—ICRISAT chickpea microsatellite), obtained from an SSR-enriched genomic library of ICC 4958. Screening of these SSR markers on a diverse panel of 48 chickpea accessions provided 147 polymorphic markers with 2–21 alleles and polymorphic information content value 0.04–0.92. Fifty-two of these markers were polymorphic between parental genotypes of the inter-specific population. We also analyzed 233 previously published (H-series) SSR markers that provided another set of 52 polymorphic markers. An additional 71 gene-based SNP markers were developed from transcript sequences that are highly conserved between chickpea and its near relative Medicago truncatula. By using these three approaches, 175 new marker loci along with 407 previously reported marker loci were integrated to yield an improved genetic map of chickpea. The integrated map contains 521 loci organized into eight linkage groups that span 2,602 cM, with an average inter-marker distance of 4.99 cM. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, and reveal extended synteny between these two species. The combined set of genetic markers and their integration into an improved genetic map should facilitate chickpea genetics and breeding, as well as translational studies between chickpea and Medicago.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-010-1265-1) contains supplementary material, which is available to authorized users.

At least 10 Dm genes conferring resistance to the oomycete downy mildew fungus Bremia lactucae map to the major resistance cluster in lettuce. We investigated the structure of this cluster in the lettuce cultivar Diana, which contains Dm3. A deletion breakpoint map of the chromosomal region flanking Dm3 was saturated with a variety of molecular markers. Several of these markers are components of a family of resistance gene candidates ( RGC2 ) that encode a nucleotide binding site and a leucine-rich repeat region. These motifs are characteristic of plant disease resistance genes. Bacterial artificial chromosome clones were identified by using duplicated restriction fragment length polymorphism markers from the region, including the nucleotide binding site-encoding region of RGC2. Twenty-two distinct members of the RGC2 family were characterized from the bacterial artificial chromosomes; at least two additional family members exist. The RGC2 family is highly divergent; the nucleotide identity was as low as 53% between the most distantly related copies. These RGC2 genes span at least 3.5 Mb. Eighteen members were mapped on the deletion breakpoint map. A comparison between the phylogenetic and physical relationships of these sequences demonstrated that closely related copies are physically separated from one another and indicated that complex rearrangements have shaped this region. Analysis of low-copy genomic sequences detected no genes, including RGC2 , in the Dm3 region, other than sequences related to retrotransposons and transposable elements. The related but divergent family of RGC2 genes may act as a resource for the generation of new resistance phenotypes through infrequent recombination or unequal crossing over. INTRODUCTIONDisease resistance genes frequently occur in tightly linked clusters (Pryor, 1987; Crute and Pink, 1996;Michelmore and Meyers, 1998). Clusters of plant resistance genes were first established by use of classic genetic techniques; detailed molecular analyses are now beginning to unravel the complexity of these loci and the underlying mechanisms determining their structure (Parniske et al., 1997;Song et al., 1997). It is becoming increasingly apparent that such clusters may be both common and complex genomic regions in plants.Clusters of resistance genes have been identified in diverse plant species. More than 30 different resistance specificities to the single fungal pathogen responsible for flax rust disease, Melampsora lini , have been mapped to five linkage groups (Flor, 1971;Islam and Shepherd, 1991). These loci exemplify two possible genetic arrangements that may exist for clusters of resistance genes: the flax L locus contains at least 13 allelic rust resistance specificities, and the more complex M locus exists as a tandem array of at least seven genes (Islam and Shepherd, 1991). In maize, multiple Rp genes, both linked and allelic, have been observed to mediate resistance to the rust fungus Puccinia sorghi ; 16 genetically separable loci were mapped to a single cluster known as th...

At least 10 Dm genes conferring resistance to the oomycete downy mildew fungus Bremia lactucae map to the major resistance cluster in lettuce. We investigated the structure of this cluster in the lettuce cultivar Diana, which contains Dm3. A deletion breakpoint map of the chromosomal region flanking Dm3 was saturated with a variety of molecular markers. Several of these markers are components of a family of resistance gene candidates ( RGC2 ) that encode a nucleotide binding site and a leucine-rich repeat region. These motifs are characteristic of plant disease resistance genes. Bacterial artificial chromosome clones were identified by using duplicated restriction fragment length polymorphism markers from the region, including the nucleotide binding site-encoding region of RGC2. Twenty-two distinct members of the RGC2 family were characterized from the bacterial artificial chromosomes; at least two additional family members exist. The RGC2 family is highly divergent; the nucleotide identity was as low as 53% between the most distantly related copies. These RGC2 genes span at least 3.5 Mb. Eighteen members were mapped on the deletion breakpoint map. A comparison between the phylogenetic and physical relationships of these sequences demonstrated that closely related copies are physically separated from one another and indicated that complex rearrangements have shaped this region. Analysis of low-copy genomic sequences detected no genes, including RGC2 , in the Dm3 region, other than sequences related to retrotransposons and transposable elements. The related but divergent family of RGC2 genes may act as a resource for the generation of new resistance phenotypes through infrequent recombination or unequal crossing over. INTRODUCTIONDisease resistance genes frequently occur in tightly linked clusters (Pryor, 1987; Crute and Pink, 1996;Michelmore and Meyers, 1998). Clusters of plant resistance genes were first established by use of classic genetic techniques; detailed molecular analyses are now beginning to unravel the complexity of these loci and the underlying mechanisms determining their structure (Parniske et al., 1997;Song et al., 1997). It is becoming increasingly apparent that such clusters may be both common and complex genomic regions in plants.Clusters of resistance genes have been identified in diverse plant species. More than 30 different resistance specificities to the single fungal pathogen responsible for flax rust disease, Melampsora lini , have been mapped to five linkage groups (Flor, 1971;Islam and Shepherd, 1991). These loci exemplify two possible genetic arrangements that may exist for clusters of resistance genes: the flax L locus contains at least 13 allelic rust resistance specificities, and the more complex M locus exists as a tandem array of at least seven genes (Islam and Shepherd, 1991). In maize, multiple Rp genes, both linked and allelic, have been observed to mediate resistance to the rust fungus Puccinia sorghi ; 16 genetically separable loci were mapped to a single cluster known as th...

The present study was carried out with the objective to validate the molecular markers, which have been previously reported to be linked to fertility restorer (Rf) gene(s) for WA-CMS lines of rice. Two mapping populations involving fertility restorer lines for WA-cytoplasm, viz.

Seed protein profiles of nine diploid species (2n = 20), ten tetraploid accessions, two synthetic amphidiploids and two autotetraploids (2n = 40) were studied using SDS-polyacrylamide gel electrophoresis. While the general profiles suggested considerable homology among these taxa in spite of speciation and ploidy differences, appreciable genetic differences were present to support the existing genomic divisions and sub-divisions in the section Arachis. A high degree of relationship was indicated between the two diploid species (A. duranensis containing the A genome and A. batizocoi (ICG 8210) containing the B genome) and tetraploids A. monticola/ A. hypogaea (2n = 40) containing AABB genome. Similar relationships were recorded between the AABB synthetic amphidiploid and the profile obtained from the mixture of protein of A. duranensis and A. batizocoi, suggesting that these two diploid species were the donors of the A and B genome, respectively, to tetraploid A. monticola/A. hypogaea.

Peacock, J. M. 1988. Proline accumulation and nitrate reductase activity in contrasting sorghum lines during mid-season drought stress. -Physiol. Plant. 74: 418-426.Six lines of sorghum {Sorghum bicolor L. Moench) with differing drought resistance (IS 22380, ICSV 213, IS 13441 and SPH 263, resistant and IS 12739 and IS 12744, susceptible) were grown under field conditions in the semi-arid tropics and analysed for proline and nitrate reductase activity (NRA; EC 1.6 6.1) during a mid-season drought. The resistant lines accumulated high levels of proline, while the susceptible lines showed no significant proline accumulation. Most of the proline was accumulated after growth of the plants had ceased. In a separate greenhouse experiment, most of the proline was found in the green rather than the fired portions of leaves. The levels returned to that of irrigated controls within 5 days of rewatering. Proline levels increased as leaf water potential and relative water content fell, and there was no apparent difference among the different sorghum lines with change in plant water status. Susceptible lines accumulated less proline than resistant lines as leaf death occurred at higher water potentials. Proline accumulation may, however, contribute to the immediate recovery of plants from drought. Leaf NRA reached high levels at about 35 days after sowing in both the stressed and irrigated plants, after which it declined. The decline in NRA was more pronounced in the stressed than in the irrigated plants and closely followed changes in the growth rate. Upon rewatering, NRA increased several-fold in all the lines and, in contrast to proline accumulation, genotypic differences in NRA were small, both during stress and upon rewatering. The high sensitivity of NRA to mild drought stress was reflected in the rapid decline of activity with small changes in leaf water potential and relative water content. The results are discussed in the light of a possible role for proline during recovery from drought, and the maintenance of NRA during stress and its recovery upon rewatering.