Alagu Manickavelu

Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change

Climate change has generated unpredictability in the timing and amount of rain, as well as extreme heat and cold spells that have affected grain yields worldwide and threaten food security. Sources of specific adaptation related to drought and heat, as well as associated breeding of genetic traits, will contribute to maintaining grain yields in dry and warm years. Increased crop photosynthesis and biomass have been achieved particularly through disease resistance and healthy leaves. Similarly, sources of drought and heat adaptation through extended photosynthesis and increased biomass would also greatly benefit crop improvement. Wheat landraces have been cultivated for thousands of years under the most extreme environmental conditions. They have also been cultivated in lower input farming systems for which adaptation traits, particularly those that increase the duration of photosynthesis, have been conserved. Landraces are a valuable source of genetic diversity and specific adaptation to local environmental conditions according to their place of origin. Evidence supports the hypothesis that landraces can provide sources of increased biomass and thousand kernel weight, both important traits for adaptation to tolerate drought and heat. Evaluation of wheat landraces stored in gene banks with highly beneficial untapped diversity and sources of stress adaptation, once characterized, should also be used for wheat improvement. Unified development of databases and promotion of data sharing among physiologists, pathologists, wheat quality scientists, national programmes, and breeders will greatly benefit wheat improvement for adaptation to climate change worldwide.

Comparative Gene Expression Analysis of Susceptible and Resistant Near-Isogenic Lines in Common Wheat Infected by Puccinia triticina

Gene expression after leaf rust infection was compared in near-isogenic wheat lines differing in the Lr10 leaf rust resistance gene. RNA from susceptible and resistant plants was used for cDNA library construction. In total, 55 008 ESTs were sequenced from the two libraries, then combined and assembled into 14 268 unigenes for further analysis. Of these ESTs, 89% encoded proteins similar to (E value of ≤10−5) characterized or annotated proteins from the NCBI non-redundant database representing diverse molecular functions, cellular localization and biological processes based on gene ontology classification. Further, the unigenes were classified into susceptible and resistant classes based on the EST members assembled from the respective libraries. Several genes from the resistant sample (14-3-3 protein, wali5 protein, actin-depolymerization factor and ADP-ribosylation factor) and the susceptible sample (brown plant hopper resistance protein, caffeic acid O-methyltransferase, pathogenesis-related protein and senescence-associated protein) were selected and their differential expression in the resistant and susceptible samples collected at different time points after leaf rust infection was confirmed by RT–PCR analysis. The molecular pathogenicity of leaf rust in wheat was studied and the EST data generated made a foundation for future studies.

Comprehensive functional analyses of expressed sequence tags in common wheat (Triticum aestivum).

About 1 million expressed sequence tag (EST) sequences comprising 125.3 Mb nucleotides were accreted from 51 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including abiotic stresses and pathogen challenges in common wheat (Triticum aestivum). Expressed sequence tags were assembled with stringent parameters after processing with inbuild scripts, resulting in 37 138 contigs and 215 199 singlets. In the assembled sequences, 10.6% presented no matches with existing sequences in public databases. Functional characterization of wheat unigenes by gene ontology annotation, mining transcription factors, full-length cDNA, and miRNA targeting sites were carried out. A bioinformatics strategy was developed to discover single-nucleotide polymorphisms (SNPs) within our large EST resource and reported the SNPs between and within (homoeologous) cultivars. Digital gene expression was performed to find the tissue-specific gene expression, and correspondence analysis was executed to identify common and specific gene expression by selecting four biotic stress-related libraries. The assembly and associated information cater a framework for future investigation in functional genomics.

Altered gene expression profiles of wheat genotypes against Fusarium head blight.

Fusarium graminearum is responsible for Fusarium head blight (FHB), which is a destructive disease of wheat that makes its quality unsuitable for end use. To understand the temporal molecular response against this pathogen, microarray gene expression analysis was carried out at two time points on three wheat genotypes, the spikes of which were infected by Fusarium graminearum. The greatest number of genes was upregulated in Nobeokabouzu-komugi followed by Sumai 3, whereas the minimum expression in Gamenya was at three days after inoculation (dai). In Nobeokabouzu-komugi, high expression of detoxification genes, such as multidrug-resistant protein, multidrug resistance-associated protein, UDP-glycosyltransferase and ABC transporters, in addition to systemic defense-related genes, were identified at the early stage of infection. This early response of the highly-resistant genotype implies a different resistance response from the other resistant genotype, Sumai 3, primarily containing local defense-related genes, such as cell wall defense genes. In Gamenya, the expression of all three functional groups was minimal. The differences in these molecular responses with respect to the time points confirmed the variation in the genotypes. For the first time, we report the nature of gene expression in the FHB-highly resistant cv. Nobeokabouzu-komugi during the disease establishment stage and the possible underlying molecular response.

Genetic diversity analysis of Afghan wheat landraces (Triticum aestivum) using DArT markers

Crop landraces represent a source of useful genes endowing tolerance to biotic and abiotic stresses, and other agronomic traits including yield. Our study involved 446 Afghan wheat (Triticum aestivum L.) landraces collected from 16 provinces during three Japanese scientific expeditions in 1955, 1967, and 1979. The landraces and varieties were genotyped using 30,000 diversity array technology (DArT) genetic markers, of which 15,817 were polymorphic. The landraces were grouped into 15 subpopulations based on population structure and phylogenetic studies. DArT markers were used to group landraces based on their origins or collection sites and to differentiate East Asian genotypes, CIMMYT lines, and modern Afghanistan cultivars from Afghan landraces. The Afghan landraces were highly diverse compared with lines from other origins. These landraces seem to possess unique genes that might allow enrichment of the global wheat gene pool and improvements in wheat production worldwide. Our next objective is to identify genotypes with promising attributes and to conduct association mapping studies focusing on biotic and abiotic stresses.

Genome-wide transcriptional profiling of wheat infected with Fusarium graminearum.

Fusarium head blight (FHB) is a destructive disease in wheat caused by Fusarium graminearum (F.g). It infects during the flowering stage favored by warm and highly humid climates. In order to understand possible wheat defense mechanism, gene expression analysis in response to F.g was undertaken in three genotypes of wheat, Japanese landrace cultivar Nobeokabouzu (highly resistant), Chinese cv. Sumai 3 (resistant) and Australian cv. Gamenya (susceptible). For microarray analysis, 3 and 7 days after inoculation (dai) samples were used in Agilent wheat custom array 4x38k. At 3 dai, the highest number of genes was up-regulated in Nobeokabouzu followed by Sumai 3 and minimum expression in Gamenya. Whereas at 7 dai, Sumai 3 expressed more genes compared to others. Further narrowing down by excluding commonly expressed genes in three genotypes and grouping according to the gene function has identified differentially high expression of genes involved in detoxification process such as multidrug resistant protein, multidrug resistance-associated protein, UDP-glycosyltransferase and ABC transporters in Nobeokabouzu at 3 dai. However in Sumai 3 many defense-related genes such as peroxidase, proteases and genes involved in plant cell wall defense at 7 dai were identified. These findings showed the difference of molecular defense mechanism among the cultivars in response to the pathogen. The complete data was accessed in NCBI GEO database with accession number GSE59721.

Molecular characterization of crossability gene Kr1 for intergeneric hybridization in Triticum aestivum (Poaceae: Triticeae)

Intergeneric hybridization is an important strategy to introgress alien genes into common wheat for its improvement. But presence of crossability barrier mechanism regulated by Kr1 gene played a major destructive role for hybridization than other reported genes. In order to know the underlying molecular mechanism and to dissect out this barrier, cDNA-AFLP (Amplified Fragment Length Polymorphism) transcriptional analysis was carried out using chromosome 5B RIL (Recombinant Inbred Line) population. Totally 14 differentially expressed fragments for Kr1 gene were identified, cloned and sequenced. Further the expression was confirmed by northern blotting analysis. Sequence analysis of the resulted clones revealed several classes of putative genes, including stress responsive, signal transduction and flowering related genes. The probable relation between other genes, Vrn1 and Ph1, located along with Kr1 gene was discussed.

Molecular evaluation of Afghan wheat landraces

The wheat landraces collected by Dr Hitoshi Kihara et al. from Afghanistan, the place of secondary origin of wheat, are an untapped genetic resource for mining novel alleles. In this study, approximately 400 landraces were collected from seven agroecological zones and characterized using diversity array technology and single-nucleotide polymorphism markers, as well as diagnostic molecular markers at important loci controlling vernalization ( Vrn ), photoperiod response ( Ppd ), grain colour ( R ), leaf rust ( Lr ), yellow rust ( Yr ), stem rust ( Sr ) and Fusarium head blight ( Fhb ). A genome-wide marker array revealed a large amount of genetic diversity among the landraces, 53% of which were winter types, 43% were either spring types or facultative and 4% were either unknown or had Vrn-A1c – a rare spring allele that needs to be confirmed with additional genotyping and phenotyping. At Ppd , 97% of the lines carried a photosensitive allele. In the case of grain colour, classification based on dominant or recessive allelic combinations revealed that approximately 39% of the population is characterized by white grain. Four gene-specific markers that were targeted to identify loci for rust and Fhb resistance enabled us to identify 17 unique landraces with known resistance genes.

Advances in Lentil Genomics

Lentil is a diploid (2n = 2X = 14) self-pollinating crop with a genome size of 4 Gbp. The use of genomics tools in lentil breeding programs has been limited, since available genomic resources are not adequate. Recent advances in high-throughput genotyping and sequencing technologies have brought in new impetus in the development of genetic and genomic resources and high resolution marker-trait association in lentil. Their integration in marker-assisted breeding is expected to improve the precision and efficiency in breeding programs with accelerated and directed genetic gains in crops like lentil. Molecular markers are expected to facilitate indirect selection for difficult traits, introgression of novel genes into adapted varieties, pyramiding genes from different sources, and combining multiple stress resistance. The present review highlights recent advances in lentil genomics and future outlook in the light of rapid advancement in the genomics tools.

Genome wide association mapping of stripe rust resistance in Afghan wheat landraces.

Mining of new genetic resources is of paramount importance to combat the alarming spread of stripe rust disease and breakdown of major resistance genes in wheat. We conducted a genome wide association study on 352 un-utilized Afghan wheat landraces against stripe rust resistance in eight locations. High level of disease variation was observed among locations and a core-set of germplasm showed consistence performance. Linkage disequilibrium (LD) decayed rapidly (R2≈0.16 at 0cM) due to germplasm peerless diversity. The mixed linear model resulted in ten marker-trait associations (MTAs) across all environments representing five QTL. The extensively short LD blocks required us to repeat the analysis with less diverse subset of 220 landraces in which R2 decayed below 0.2 at 0.3cM. The subset GWAS resulted in 36 MTAs clustered in nine QTL. The subset analysis validated three QTL previously detected in the full list analysis. Overall, the study revealed that stripe rust epidemics in the geographical origin of this germplasm through time have permitted for selecting novel resistance loci.