Search

The construction of high density genetic linkage map provides a powerful tool to detect and map quantitative trait loci (QTLs) controlling agronomically important traits. In this study, simple sequence repeat (SSR) markers and Illumina 9K iSelect single nucleotide polymorphism (SNP) genechip were employed to construct one genetic linkage map of common wheat ( Triticum aestivum L.) using 191 recombinant inbred lines (RILs) derived from cross Yu 8679×Jing 411. This map included 1 901 SNP loci and 178 SSR loci, covering 1 659.9 cM and 1 000 marker bins, with an average interval distance of 1.66 cM. A, B and D genomes covered 719.1, 703.5 and 237.3 cM, with an average interval distance of 1.66, 1.45 and 2.9 cM, respectively. Notably, the genetic linkage map covered 20 chromosomes, with the exception of chromosome 5D. Bioinformatics analysis revealed that 1 754 (92.27%) of 1 901 mapped SNP loci could be aligned to 1 215 distinct wheat unigenes, among which 1 184 (97.4%) were located on one single chromosome, and the rest 31 (2.6%) were located on 2 to 3 chromosomes. By performing in silico comparison, 214 chromosome deletion bin-mapped expressed sequence tags (ESTs), 1 043 Brachypodium genes and 1 033 rice genes were further added onto the genetic linkage map. This map not only integrated genetic and physical maps, SSR and SNP loci, respectively, but also provided the information of Brachypodium and rice genes corresponding to 1 754 SNP loci. Therefore, it will be a useful tool for comparative genomics analysis, fine mapping of QTL/gene controlling agronomically important traits and marker-assisted selection breeding in wheat.

Through bioinformatic data mining, 10 SnRK2 and 31 CIPK genes were identified from sorghum genome. They are unevenly distributed in the sorghum chromosomes. Most SnRK2 genes have 8 introns, while the CIPK genes have a few (no intron or less than 3 introns) or more than 10 introns. Phylogenetic analysis revealed that SnRK2 genes belong to one cluster and CIPK genes form the other independent cluster. The sorghum SnRK2s are subgrouped into three parts, and CIPK into five parts. More than half SnRK2 and CIPK genes present in homologous pairs, suggesting gene duplication may be due to the amplification of SnRK family genes. The kinase domains of SnRK2 family are highly conserved with 88.40% identity, but those of the CIPK family are less conserved with 63.72% identity. And the identity of sorghum CBL- interacting NAF domains of CIPKs is 61.66%. What's more, regarding to the sorghum SnRK2 and CIPK kinases, they are characterized with distinct motifs and their subcellular localization is not necessarily the same, which suggests they may be divergent in functions. Due to less conserved sequences, complex subcellular localization, and more family members, sorghum CIPK genes may play more flexible and multiple biological functions. According to the phylogenetic analysis of SnRK genes and SnRK functional studies in other plants, it is speculated that sorghum SnRK2 and CIPK genes may play important roles in stress response, growth and development.

Fungal diseases cause serious yield losses in wheat ( Triticum aestivum L.) worldwide. Numerous genes involved in the wheat–pathogen interactions have been identified, which include pathogenesis related (PR) genes and antifungal hydrolases, such as glucanase and chitinase genes. Recently, there has been increasing evidence of the potential involvement of 1,3-β-glucanase in defense against fungal infection. In this study, a cDNA encoding a 1,3-β-glucanase, designated TaGlc2 , was identified from a wheat cDNA library. The deduced peptide sequence of TaGlc2 is similar to a glycoside hydrolase family 17. Using real-time PCR, the expression pattern of TaGlc2 in wheat seedlings inoculated with powdery mildew pathogen ( Erysiphe graminis ) was determined. The results showed that TaGlc2 is inducible in response to fungal infection. The 5′ genomic region of TaGlc2 was isolated. This gene contains some cis -elements that are reported to be involved in pathogenesis response.

The availability of high-throughput genotyping technologies and microarray assays has allowed researchers to investigate genetic variations that influence levels of gene expression. Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression. Similar to traditional QTL studies, the main goal of eQTL is to identify the genomic locations to which the expression traits are linked. Although microarrays provide the expression data of thousands of transcripts, standard QTL mapping methods, which are able to handle at most tens of traits, cannot be applied directly. As a result, it is necessary to consider the statistical principles involved in the design and analysis of these experiments. In this paper, we reviewed individual selection, experimental design of microarray, normalization of gene expression data, mapping methods, and explaining of results and proposed potential methodological problems for such analyses. Finally, we discussed the applications of this integrative genomic approach to estimate heritability of transcripts, identify candidate genes, construct gene networks, and understand interactions between genes, genes and environments.

Two SSR molecular markers, genomic-SSR and EST (expressed sequence tagged)-SSR, were used to measure the genetic diversity among 18 accessions of common wheat with known pedigrees, which were collected from winter wheat production region in Northern China. In addtion, the genetic diversity revealed by pedigree, EST-SSR and genomic-SSR was also compared. The results showed that the average number of alleles per genomic-SSR locus is 3.34, which is higher than that of EST-SSR (2.31), indicating that genomic-SSR is more polymorphic than EST-SSR. Genomic-SSR and EST-SSR were used to calculate the genetic distance (GD) in different materials. The mean GD value of EST-SSR for the 18 wheat genotypes is 0.3996,which is lower than that of genomic-SSR (0.5458). At the locus level, the mean GD calculated using pedigree information is higher (0. 9716) than that of genomic-SSR and EST-SSR markers (0.5458 and 0.3996). Therefore, although polymorphism of EST-SSR is low as compared to genomic SSR,it provides a more accurate evaluation of genetic relationship, especially when accessions are very closely related in pedigree. The strategy for improving the genetic diversity of wheat was also discussed.

In order to understand molecular basis of heterosis, mRNA differential display was used to analyze the differences in gene expression between seeds of 18 reciprocal hybrids and their 6 parents at 6th day after pollination. The relationship between gene expression patterns and heterosis was determined. Only bands that can be repeated in duplicate PCR were used for analysis so as to reduce false positive bands. Among the total of 2,025 bands displayed, 1,386 bands (68.43%) were reproducible. Eight patterns (fifteen kinds) of gene expression were observed, which include: (1) bands occurring in only one parent (two kinds); (2) bands observed in both hybrids and one parent (two kinds); (3) bands detected in parents and one hybrid (two kinds); (4) bands displayed in only one hybrid (two kinds); (5) bands revealed in one hybrid and its corresponding female (two kinds) or male (two kinds) parent; (6) bands visualized in only both hybrids (one kind); (7) bands occurring in only parents (one kind); (8) bands observed in parents and both hybrids (one kind). Our results indicate that differences of gene expression between hybrids and their parents are very obvious. The percentages of bands observed in only both hybrids and in only both parents are lower. The analysis shows that bands observed in parents and both hybrids are not correlated with all nine agronomic traits, which indicates differentially expressed genes are mainly responsible for the observed heterosis. At least one pattern of differential gene expression is significantly correlated with nine agronomic traits. Silenced bands in hybrid (which include bands occurring in only one parent, bands detected in both parents and one hybrid and bands in only parents) and bands present in one hybrid and its corresponding female or male parent are likely to play important roles in heterosis. These results suggest that early seed development could be closely related to heterosis.

Simple sequence repeat (SSR) molecular marker was used to measure the genetic diversity of D-genome in 26 synthesized hexaploid wheat (AABBDD) introduced from CIMMYT. Twenty-three D-genome specific SSR primers were selected for PCR amplification, among which 22 primers can detect polymorphism. A total of 92 alleles were identified at 23 loci using the above SSR primers, with an average of 4 alleles per locus. The 92 alleles were used to calculate Nei's similarity index (GS) and the genetic distance (GD). It was also found that the mean genetic distance between 26 synthesized hexaploid wheat was 0.4955, which was obviously high. From the above results, it can be indicated that the genetic variation of D-genome in synthesized hexaploid wheat was abundant and could be used to improve the genetic diversity in wheat breeding. Interestingly, synthesized hexaploid wheat 17 and 18 shared the same D-genome donor, but three of 23 detected SSR loci were polymorphic between the two materials. Therefore, during the period of allopolyploidization, there was genetic differentiation in repeat region of donor genome.

It is important to estimate the genetic diversity between the parents for improving the heterosis of hybrid wheat. In this study, ISSR(inter-simple sequence repeat) marker was used to measure the genetic diversity within and among common wheat (Triticum aestivum L.), spelt (Triticum spelta L.), compactum (Triticum compactum Host.) and progeny of foreign wheat-based recurrent selection, and the possibility of establishing the new heterotic group was also assessed. Forty seven genotypes were used for ISSR analysis, which included 14 common wheat, 10 spelt wheat, 11 compactum and 12 progeny of recurrent selection. Eleven of 33 ISSR primers that can produce distinguishable bands were selected for PCR amplification. A total of 238 bands were amplified, among which 207 (87%) bands were polymorphic. The polymorphic bands amplified by each primer ranged from 11 to 38, with an averaged of 18.8. The percentage of polymorphic band (80.3%) in common wheat was higher than that in progeny of recurrent selection (78.7%), spelt (75.0%) and compactum (74.9%). The 238 polymorphic products were used to calculate Nei's similarity index (GS) and the genetic distance (GD). It was found that the mean genetic distance between different wheat types (0.3115-0.3442) was obviously higher than that within common wheat (0.2743), spelt (0.2351), compactum (0.2622). In addition, progeny of recurrent selection also showed much higher genetic distance with other three wheat types (0.3217, 0.3256, 0.3198). The cluster analysis was performed based on the genetic distance (GD) matrix by using UPGMA method. Common wheat, spelt, compactum and progeny of recurrent selection were classified into four different groups. In this study, ISSR marker was firstly used to assess genetic diversity among common wheat, spelt, compactum and progeny of recurrent selection, and can differentiate the wheat cultivars (lines) that selected from the same cross combination. It was concluded that spelt, compactum and progeny of recurrent selection can be used to diversify the genetic basis for hybrid wheat breeding and improve heterosis. It is possible to establish the wheat heterotic group by ISSR marker.