ABA receptors (PYR/PYL/RCAR) play a central role in the water loss control of plants.  A previous report indicated that TaPYL4 is a critical gene in wheat that improves grain production under drought conditions and increases water use efficiency.  In this study, we analyzed the sequence polymorphisms and genetic effects of TaPYL4s.  Based on isolated TaPYL4 genes from chromosomes 2A, 2B and 2D, three haplotypes were detected in the promoter region of TaPYL4-2A, and two haplotypes were present in TaPYL4-2B and TaPYL4-2D, respectively.  Marker/trait association analysis indicated that TaPYL4-2A was significantly associated with plant height in 262 Chinese wheat core collection accessions, as well as the drought tolerance coefficient (DTC) for plant height in 239 wheat varieties from Shanxi Province in multiple environments.  However, the frequencies of favored drought-tolerant haplotype TaPYL4-2A-Hap2 were considerably low, accounting for only 10%, and lines with this certain Hap could be reserved in the breeding program.  TaPYL4-2B was significantly associated with grain number, and the favored haplotype TaPYL4-2B-Hap1 was the dominant allele of above 90% in the collection.  For TaPYL4-2D, there were no significant differences in these traits between the two haplotypes in either of the two panels.  These results indicate that variation might lead to functional differentiation among the homoeologs and the haplotypes had undergone artificial selection during breeding.  Two molecular markers developed to distinguish these haplotypes could be used for breeding in water-limited regions.

Resistance gene analog (RGA) screening of mapped disease-resistant genes not only helps to clone these genes but also helps to develop efficient molecular markers for resistance breeding. The present study focused on the PmU region located on chromosome 7A^uL of Triticum urartu, and recently, a nucleotide binding site (NBS)-encoding gene, Pm60, was cloned from the same chromosome arm. In this research, NBS, protein kinase (PK), and ATP-binding cassette (ABC), the three disease resistance-related gene families, were analyzed within PmU region by using informatics tools, and an expression experiment was conducted to verify their functions in vivo. Comparative genomic analysis revealed that 126 RGAs were included on chromosome 7A^uL, and 30 of the RGAs as well as Pm60 were found in the PmU region. Transcriptome database analysis of T. urartu revealed 14 PmU-RGAs with expression data, and three PmU-NBSs exhibited significant changes in expression after inoculation with Blumeria graminis f. sp. tritici (Bgt); TRIUR3_14879 was up-regulated, while TRIUR3_00450 and TRIUR3_06270 were down-regulated. Cluster analysis showed that these three PmU-NBSs were clustered far from the cloned wheat resistance genes. Then, qRT-PCR was performed to investigate the expression of 14 PmU-RGAs and Pm60 after inoculation with Bgt race E09; the results showed that Pm60 was specifically expressed in UR206 which carrying PmU, but not in susceptible UR203; while TRIUR3_14879 was significantly up-regulated and TRIUR3_00450 was downregulated in UR206 after inoculation. These results indicated that PmU is Pm60, and TRIUR3_14879 and TRIUR3_00450 may also be involved in the defense against Bgt.

    The R2R3-MYB genes make up one of the largest transcription factor families in plants, and play regulatory roles in various biological processes such as development, metabolism and defense response.  Although genome-wide analyses of this gene family have been conducted in several species, R2R3-MYB genes have not been systematically analyzed in Medicago truncatula, a sequenced model legume plant.  Here, we performed a comprehensive, genome-wide computational analysis of the structural characteristics, phylogeny, functions and expression patterns of M. truncatula R2R3-MYB genes.  DNA binding domains are highly conserved among the 155 putative MtR2R3-MYB proteins that we identified.  Chromosomal location analysis revealed that these genes were distributed across all eight chromosomes.  Results showed that the expansion of the MtR2R3-MYB family was mainly attributable to segmental duplication and tandem duplication.  A comprehensive classification was performed based on phylogenetic analysis of the R2R3-MYB gene families in M. truncatula, Arabidopsis thaliana and other plant species.  Evolutionary relationships within clades were supported by clade-specific conserved motifs outside the MYB domain.  Species-specific clades have been gained or lost during evolution, resulting in functional divergence.  Also, tissue-specific expression patterns were investigated.  The functions of stress response-related clades were further verified by the changes in transcript levels of representative R2R3-MYB genes upon treatment with abiotic and biotic stresses.  This study is the first report on identification and characterization of R2R3-MYB gene family based on the genome of M. truncatula, and will facilitate functional analysis of this gene family in the future.