Genetic mapping of the wheat dimeric α-amylase inhibitor multi-gene family using allele-specific primers based on intergenomic SNPs

Single nucleotide polymorphisms (SNPs) identified in EST sequences can be used to map expressed genes. Though SNPs are useful markers for genetic mapping, SNP mapping of genes in common wheat is challenging because the genetic complement of wheat consists of three closely related genomes (designated A, B, and D), and most genes are present in triplicate sets. Mapping multi-gene family members is further complicated by the fact that it is difficult to distinguish SNP differences between the various paralogs from those between the different genomes. We have developed a PCR-based method for assigning wheat EST sequences to their proper genetic loci by first identifying and mapping SNPs that distinguish the three genomes. To develop this method, we focused on EST sequences encoding the dimeric α-amylase inhibitors (WDAI), The WDAI coding regions of hexaploid wheat were aligned. The sequences were classified into three groups based on nucleotide variations. Twenty-two SNPs were identified that distinguish the three groups. Group-specific primers based on these SNPs were designed to permit selective amplification of each group. The chromosomal location of each group was then determined using Group 3 ditelosomic lines of Chinese Spring. Groups 1 and 2 were assigned to chromosome locations 3DS and 3BS, respectively, whereas no sequence could be assigned to 3AS. A remarkable feature of this method is the ability to discriminate the location of homoeologous multigenes in the three genomes of wheat. This strategy can be useful for assigning unknown wheat EST sequences to specific chromosomes.     

Linked gene networks involved in nitrogen and carbon metabolism and levels of water-soluble carbohydrate accumulation in wheat stems

High levels of water-soluble carbohydrates (WSC) provide an important source of stored assimilate for grain filling in wheat. To better understand the interaction between carbohydrate metabolism and other metabolic processes associated with the WSC trait, a genome-wide expression analysis was performed using eight field-grown lines from the high and low phenotypic tails of a wheat population segregating for WSC and the Affymetrix wheat genome array. The 259 differentially expressed probe sets could be assigned to 26 functional category bins, as defined using MapMan software. There were major differences in the categories to which the differentially expressed probe sets were assigned; for example, probe sets upregulated in high relative to low WSC lines were assigned to category bins such as amino acid metabolism, protein degradation and transport and to be involved in starch synthesis-related processes (carbohydrate metabolism bin), whereas downregulated probe sets were assigned to cell wall-related bins, amino acid synthesis and stress and were involved in sucrose breakdown. Using the set of differentially expressed genes as input, chemical–protein network analyses demonstrated a linkage between starch and N metabolism via pyridoxal phosphate. Twelve C and N metabolism-related genes were selected for analysis of their expression response to varying N and water treatments in the field in the four high and four low WSC progeny lines; the two nitrogen/amino acid metabolism genes demonstrated a consistent negative association between their level of expression and level of WSC. Our results suggest that the assimilation of nitrogen into amino acids is an important factor that influences the levels of WSC in the stems of field-grown wheat.     

Correlated clustering and virtual display of gene expression patterns in the wheat life cycle by large-scale statistical analyses of expressed sequence tags

Compared to rice, wheat exhibits characteristic growth habits and contains complex genome constituents. To assess global changes in gene expression patterns in the wheat life cycle, we conducted large-scale analysis of expressed sequence tags (ESTs) in common wheat. Ten wheat tissues were used to construct cDNA libraries: crown and root from 14-day-old seedlings; spikelet from early and late flowering stages; spike at the booting stage, heading date and flowering date; pistil at the heading date; and seeds at 10 and 30 days post-anthesis. Several thousand colonies were randomly selected from each of these 10 cDNA libraries and sequenced from both 5' and 3' ends. Consequently, a total of 116 232 sequences were accumulated and classified into 25 971 contigs based on sequence homology. By computing abundantly expressed ESTs, correlated expression patterns of genes across the tissues were identified. Furthermore, relationships of gene expression profiles among the 10 wheat tissues were inferred from global gene expression patterns. Genes with similar functions were grouped with one another by clustering gene expression profiles. This technique might enable estimation of the functions of anonymous genes. Multidimensional analysis of EST data that is analogous to the microarray experiments may offer new approaches to functional genomics of plants.     

Molecular Characterization and Expression Analysis of Triticum aestivum Squamosa‐Promoter Binding Protein‐Box Genes Involved in Ear Development

Wheat (Triticum aestivum L.) is one of the most important crops in the world. Squamosa‐promoter binding protein (SBP)‐box genes play a critical role in regulating flower and fruit development. In this study, 10 novel SBP‐box genes (TaSPL genes) were isolated from wheat ((Triticum aestivum L.) cultivar Yanzhan 4110). Phylogenetic analysis classified the TaSPL genes into five groups (G1–G5). The motif combinations and expression patterns of the TaSPL genes varied among the five groups with each having own distinctive characteristics: TaSPL20/21 in G1 and TaSPL17 in G2 mainly expressed in the shoot apical meristem and the young ear, and their expression levels responded to development of the ear; TaSPL6/15 belonging to G3 were upregulated and TaSPL1/23 in G4 were downregulated during grain development; the gene in G5 (TaSPL3) expressed constitutively. Thus, the consistency of the phylogenetic analysis, motif compositions, and expression patterns of the TaSPL genes revealed specific gene structures and functions. On the other hand, the diverse gene structures and different expression patterns suggested that wheat SBP‐box genes have a wide range of functions. The results also suggest a potential role for wheat SBP‐box genes in ear development. This study provides a significant beginning of functional analysis of SBP‐box genes in wheat.