Molecular evolution of dimeric alpha-amylase inhibitor genes in wild emmer wheat and its ecological association

Optimisation of the production of corn amylase flour from corn Atp and Kassaï varieties for the fluidification and energy density increase of cassava gruel

The energy density of the complementary gruels can be increased by the use of sprouted flours. This led us to determine the conditions for obtaining and using sprouted corn flour for optimal fluidification of fermented cassava flour gruels. To do this, the germinated corn flour (GCF) varieties Atp and Kassaï was produced according to the response surface methodology and the Doehlert plan was used with factors such as soaking (12-48 h) and germination (24-96 h) times. Once obtained, these GCF were used to increase the energy density of cassava flour gruels with flow velocity as response. The Doehlert plan was also used with fermented cassava flour concentration (17.5-30 %) and optimised sprouted corn flour mass (1-5 g) as factors. The experimental design that had been performed indicated that the effectiveness of corn amylase flour to fluidify the gruels depends not only to the conditions of production (soaking and germination) (p < 0.05) but also their incorporation during the preparation (corn amylase-fermented cassava flour) (p < 0.05). The rich corn amylase flour can be obtained by soaking Kassaï and Atp varieties for 20 h and 28 h respectively and germinated for 90.82 h. Application of these GCF during the preparation of fermented cassava flour gruels has shown that to obtain gruels with flow velocities between 100-160 mm/30s, it was necessary to couple 1.16 g of sprouted corn flour variety Kassaï for 26.23 % of fermented cassava flour and 1.12 g of corn flour variety Atp for 25.94 % of fermented cassava flour. The use of these couples has made it possible to multiply the energy density of the gruels by 6.55 and 6.49, respectively. In view of these results, it is therefore advisable to use the germinated corn flours produced under the conditions obtained to fluidise and increase the energy density of the fermented cassava gruels.

Current Progress in Understanding and Recovering the Wheat Genes Lost in Evolution and Domestication

The modern cultivated wheat has passed a long evolution involving origin of wild emmer (WEM), development of cultivated emmer, formation of spelt wheat and finally establishment of modern bread wheat and durum wheat. During this evolutionary process, rapid alterations and sporadic changes in wheat genome took place, due to hybridization, polyploidization, domestication, and mutation. This has resulted in some modifications and a high level of gene loss. As a result, the modern cultivated wheat does not contain all genes of their progenitors. These lost genes are novel for modern wheat improvement. Exploring wild progenitor for genetic variation of important traits is directly beneficial for wheat breeding. WEM wheat (Triticum dicoccoides) is a great genetic resource with huge diversity for traits. Few genes and quantitative trait loci (QTL) for agronomic, quantitative, biotic and abiotic stress-related traits have already been mapped from WEM. This resource can be utilized for modern wheat improvement by integrating identified genes or QTLs through breeding.

New insights into the evolution of wheat avenin-like proteins in wild emmer wheat (Triticum dicoccoides)

Fifteen full-length wheat grain avenin-like protein coding genes (TaALP) were identified on chromosome arms 7AS, 4AL, and 7DS of bread wheat with each containing five genes. Besides the a- and b-type ALPs, a c type was identified in the current paper. Both a and b types have two subunits, named x and y types. The five genes on each of the three chromosome arms consisted of two x-type genes, two y-type genes, and one c-type gene. The a-type genes were typically of 520 bp in length, whereas the b types were of 850 bp in length, and the c type was of 470 bp in length. The ALP gene transcript levels were significantly up-regulated in Blumeria graminis f. sp. tritici (Bgt)-infected wheat grain caryopsis at early grain filling. Wild emmer wheat [(WEW), Triticum dicoccoides] populations were focused on in our paper to identify allelic variations of ALP genes and to study the influence of natural selection on certain alleles. Consequently, 25 alleles were identified for TdALP-bx-7AS, 13 alleles were identified for TdALP-ax-7AS, 7 alleles were identified for TdALP-ay-7AS, and 4 alleles were identified for TdALP-ax-4AL Correlation studies on TdALP gene diversity and ecological stresses suggested that environmental factors contribute to the ALP polymorphism formation in WEW. Many allelic variants of ALPs in the endosperm of WEW are not present in bread wheat and therefore could be utilized in breeding bread wheat varieties for better quality and elite plant defense characteristics.

Drought tolerance in modern and wild wheat

The genus Triticum includes bread (Triticum aestivum) and durum wheat (Triticum durum) and constitutes a major source for human food consumption. Drought is currently the leading threat on world's food supply, limiting crop yield, and is complicated since drought tolerance is a quantitative trait with a complex phenotype affected by the plant's developmental stage. Drought tolerance is crucial to stabilize and increase food production since domestication has limited the genetic diversity of crops including wild wheat, leading to cultivated species, adapted to artificial environments, and lost tolerance to drought stress. Improvement for drought tolerance can be achieved by the introduction of drought-grelated genes and QTLs to modern wheat cultivars. Therefore, identification of candidate molecules or loci involved in drought tolerance is necessary, which is undertaken by "omics" studies and QTL mapping. In this sense, wild counterparts of modern varieties, specifically wild emmer wheat (T. dicoccoides), which are highly tolerant to drought, hold a great potential. Prior to their introgression to modern wheat cultivars, drought related candidate genes are first characterized at the molecular level, and their function is confirmed via transgenic studies. After integration of the tolerance loci, specific environment targeted field trials are performed coupled with extensive analysis of morphological and physiological characteristics of developed cultivars, to assess their performance under drought conditions and their possible contributions to yield in certain regions. This paper focuses on recent advances on drought related gene/QTL identification, studies on drought related molecular pathways, and current efforts on improvement of wheat cultivars for drought tolerance.

Genome diversity in wild grasses under environmental stress

Patterns of diversity distribution in the Isa defense locus in wild-barley populations suggest adaptive selection at this locus. The extent to which environmental selection may act at additional nuclear-encoded defense loci and within the whole chloroplast genome has now been examined by analyses in two grass species. Analysis of genetic diversity in wild barley (Hordeum spontaneum) defense genes revealed much greater variation in biotic stress-related genes than abiotic stress-related genes. Genetic diversity at the Isa defense locus in wild populations of weeping ricegrass [Microlaena stipoides (Labill.) R. Br.], a very distant wild-rice relative, was more diverse in samples from relatively hotter and drier environments, a phenomenon that reflects observations in wild barley populations. Whole-chloroplast genome sequences of bulked weeping ricegrass individuals sourced from contrasting environments showed higher levels of diversity in the drier environment in both coding and noncoding portions of the genome. Increased genetic diversity may be important in allowing plant populations to adapt to greater environmental variation in warmer and drier climatic conditions.

Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat

Sucrose non-fermenting1-related protein kinase 2 (SnRK2) plays a key role in plant stress signaling transduction pathways. In this study, one copy of TaSnRK2.7, a SnRK2 member of common wheat, was isolated and characterized for nucleotide diversity among 45 wheat accessions with different stress-response features. Most of the accessions were elite wheat cultivars, which had been subject to population bottlenecks and intensive selection during breeding. Nucleotide and haplotype diversity across the entire TaSnRK2.7-A region was 0.00076 and 0.590, respectively, and diversity in non-coding regions was higher than that in coding regions. Sliding-window analysis showed variable levels of nucleotide variation along the entire TaSnRK2.7-A region; the sixth intron and ninth exon represented variation-enriched regions. As predicted, neutrality tests revealed that population bottlenecks or purifying selection had acted on the TaSnRK2.7-A gene, a relatively conserved gene. Furthermore, strong linkage disequilibrium between SNP loci extends across the entire TaSnRK2.7-A region. These findings demonstrate that the TaSnRK2.7-A genomic region has evolved under extensive selection pressure during crop breeding.

Molecular characterization and functional analysis of elite genes in wheat and its related species

The tribe Triticeae includes major cereal crops (bread wheat, durum wheat, triticale, barley and rye), as well as abundant forage and lawn grasses. Wheat and its wild related species possess numerous favourable genes for yield improvement, grain quality enhancement, biotic and abiotic stress resistance, and constitute a giant gene pool for wheat improvement. In recent years, significant progress on molecular characterization and functional analysis of elite genes in wheat and its related species have been achieved. In this paper, we review the cloned functional genes correlated with grain quality, biotic and abiotic stress resistance, photosystem and nutrition utilization in wheat and its related species.

Finger millet: Eleusine coracana

Finger millet (Eleusine coracana) is a grass crop grown in Africa, India Nepal, and many countries of Asia. The plant and grain is resistant to drought, pests, and pathogens. It is rich in polyphenols and particularly in calcium. The double headed trypsin, α-amylase inhibitor from this grain has been isolated and characterized extensively. One major use for the grain is the making of fermented beverages after malting. α-Amylase and β-amylase are produced during germination. Food made from malted ragi is traditionally used for weaning and has been the source of low viscosity weaning foods that can deliver more energy per feed than those based on gelatinized starch. There is some evidence that foods from finger millet have a low gylcaemic index and are good for diabetic patients. Decortication, puffing, extrusion, and expansion are some of the new uses that the grain has been put to.

The impact of single nucleotide polymorphism in monomeric alpha-amylase inhibitor genes from wild emmer wheat, primarily from Israel and Golan

Background

Various enzyme inhibitors act on key insect gut digestive hydrolases, including alpha-amylases and proteinases. Alpha-amylase inhibitors have been widely investigated for their possible use in strengthening a plant's defense against insects that are highly dependent on starch as an energy source. We attempted to unravel the diversity of monomeric alpha-amylase inhibitor genes of Israeli and Golan Heights' wild emmer wheat with different ecological factors (e.g., geography, water, and temperature). Population methods that analyze the nature and frequency of allele diversity within a species and the codon analysis method (comparing patterns of synonymous and non-synonymous changes in protein coding sequences) were used to detect natural selection.

Results

Three hundred and forty-eight sequences encoding monomeric alpha-amylase inhibitors (WMAI) were obtained from 14 populations of wild emmer wheat. The frequency of SNPs in WMAI genes was 1 out of 16.3 bases, where 28 SNPs were detected in the coding sequence. The results of purifying and the positive selection hypothesis (p < 0.05) showed that the sequences of WMAI were contributed by both natural selection and co-evolution, which ensured conservation of protein function and inhibition against diverse insect amylases. The majority of amino acid substitutions occurred at the C-terminal (positive selection domain), which ensured the stability of WMAI. SNPs in this gene could be classified into several categories associated with water, temperature, and geographic factors, respectively.

Conclusions

Great diversity at the WMAI locus, both between and within populations, was detected in the populations of wild emmer wheat. It was revealed that WMAI were naturally selected for across populations by a ratio of dN/dS as expected. Ecological factors, singly or in combination, explained a significant proportion of the variations in the SNPs. A sharp genetic divergence over very short geographic distances compared to a small genetic divergence between large geographic distances also suggested that the SNPs were subjected to natural selection, and ecological factors had an important evolutionary role in polymorphisms at this locus. According to population and codon analysis, these results suggested that monomeric alpha-amylase inhibitors are adaptively selected under different environmental conditions.

Drought and salt tolerances in wild relatives for wheat and barley improvement

Drought and salinity are the major abiotic stresses that dramatically threaten the food supply in the world. Tribe Triticeae, including wheat and barley, possesses tremendous potential for drought and salt tolerance that has been extensively and practically identified, tested, and transferred to wheat cultivars with proven expression of tolerance in experimental trials. Triticum dicoccoides and Hordeum spontaneum, the progenitors of cultivated wheat and barley, have adapted to a broad range of environments and developed rich genetic diversities for drought and salt tolerances. Drought- and salt-tolerant genes and quantitative trait loci (QTLs) have been identified in T. dicoccoides and H. spontaneum and have great potential in wheat and barley improvement. Advanced backcross QTL analysis, the introgression libraries based on wild wheat and wild barley as donors, and positional cloning of natural QTLs will play prevailing roles in elucidating the molecular control of drought and salt tolerance. Combining tolerant genes and QTLs in crop breeding programs aimed at improving tolerance to drought and salinity will be achieved within a multidisciplinary context. Wild genetic resistances to drought and salinity will be shifted in the future from field experiments to the farmer.

EST-SSR diversity correlated with ecological and genetic factors of wild emmer wheat in Israel

The differentiation of genetic diversity was estimated among 15 wild emmer wheat (Triticum dicoccoides) populations of the macrogeographic scale in Israel by 25 EST-SSR markers. A total of 92 EST-SSR alleles were detected, and the number of alleles ranged from 1 to 7 with an average of 3.68 per locus. Allele numbers and the polymorphic information content (PIC)value of EST-SSR loci on the B genome were higher than those on the A genome. The genetic similarity coefficient (GS)varied from 0.189 to 0.966, and all genotypes were clustered into four major groups. The population Mt. Gerizim had the highest genetic variations, whereas the population Beit-Oren had the lowest genetic variations. Most of genetic variance existed within populations was observed based on the coefficient of gene differentiation (F(ST)=0.355). The value of genetic distance (D) between the populations varied from 0.112 to 0.672 with an average of 0.406, and the results of Mantel test(r=0.104, p=0.809) showed that the estimates of genetic distance were geographically independent. The values of Nei's gene diversity (He) and Shannon's information index (I) correlated negatively with the temperature factor: mean January temperature (Tj), whereas they correlated positively with another factor: mean number of Sharav days (Sh). The correlation matrix between He in the EST-SSRs and climatic variables contained 37 significant (pB0.05) correlations. The present study established that T. dicoccoides in Israel had a considerable amount of genetic variations at EST-SSR loci at least partly correlated with ecological factors. These results suggested that EST-SSR diversity is adaptive by natural selection and influenced by both internal and external factors and their interactions.