Livinus Emebiri

Association mapping for soilborne pathogen resistance in synthetic hexaploid wheat

Soilborne pathogens such as cereal cyst nematode (CCN; Heterodera avenae) and root lesion nematode (Pratylenchus neglectus; PN) cause substantial yield losses in the major cereal-growing regions of the world. Incorporating resistance into wheat cultivars and breeding lines is considered the most cost-effective control measure for reducing nematode populations. To identify loci with molecular markers linked to genes conferring resistance to these pathogens, we employed a genome-wide association approach in which 332 synthetic hexaploid wheat lines previously screened for resistance to CCN and PN were genotyped with 660 Diversity Arrays Technology (DArT) markers. Two sequence-tagged site markers reportedly linked to genes known to confer resistance to CCN were also included in the analysis. Using the mixed linear model corrected for population structure and familial relatedness (Q+K matrices), we were able to confirm previously reported quantitative trait loci (QTL) for resistance to CCN and PN in bi-parental crosses. In addition, we identified other significant markers located in chromosome regions where no CCN and PN resistance genes have been reported. Seventeen DArT marker loci were found to be significantly associated with CCN and twelve to PN resistance. The novel QTL on chromosomes 1D, 4D, 5B, 5D and 7D for resistance to CCN and 4A, 5B and 7B for resistance to PN are suggested to represent new sources of genes which could be deployed in further wheat improvement against these two important root diseases of wheat.

Genetic control of grain yield and grain physical characteristics in a bread wheat population grown under a range of environmental conditions

Key messageGenetic analysis of the yield and physical quality of wheat revealed complex genetic control, including strong effects of photoperiod-sensitivity loci.AbstractEnvironmental conditions such as moisture deficit and high temperatures during the growing period affect the grain yield and grain characteristics of bread wheat (Triticum aestivum L.). The aim of this study was to map quantitative trait loci (QTL) for grain yield and grain quality traits using a Drysdale/Gladius bread wheat mapping population grown under a range of environmental conditions in Australia and Mexico. In general, yield and grain quality were reduced in environments exposed to drought and/or heat stress. Despite large effects of known photoperiod-sensitivity loci (Ppd-B1 and Ppd-D1) on crop development, grain yield and grain quality traits, it was possible to detect QTL elsewhere in the genome. Some of these QTL were detected consistently across environments. A locus on chromosome 6A (TaGW2) that is known to be associated with grain development was associated with grain width, thickness and roundness. The grain hardness (Ha) locus on chromosome 5D was associated with particle size index and flour extraction and a region on chromosome 3B was associated with grain width, thickness, thousand grain weight and yield. The genetic control of grain length appeared to be largely independent of the genetic control of the other grain dimensions. As expected, effects on grain yield were detected at loci that also affected yield components. Some QTL displayed QTL-by-environment interactions, with some having effects only in environments subject to water limitation and/or heat stress.

Genetic variation and possible SNP markers for breeding wheat with low-grain asparagine, the major precursor for acrylamide formation in heat-processed products

BACKGROUND In products made from wheat (Triticum aestivum) flour, acrylamide formation is almost exclusively determined by the level of free asparagine in the grain. Genetic variability for grain asparagine content was evaluated in order to assess the potential for acrylamide mitigation by breeding. RESULTS Free asparagine levels in the grains of 92 varieties varied from 137 to 471 mg kg⁻¹, representing an approximate threefold difference between the low- and high-asparagine genotypes. Heritability was low, with a value of 32%, indicating that breeding cultivars with inherently low grain asparagine would be a challenge. A genome-wide scan with single-nucleotide polymorphism (SNP) markers identified nine SNPs that were significantly (P < 0.001) associated with variation in free asparagine. The significant SNPs were localized on chromosome 5A, and explained between 14% and 24% of the observed variation. These putative SNPs are candidates for further studies to develop molecular markers. CONCLUSION Significant genetic variation exists for reducing acrylamide precursors in wheat flour, indicating that breeding and genetics could play an important role in mitigating the acrylamide risk in wheat products. The study identified a region on chromosome 5A that could provide a basis for further research to develop functional markers.

A SNP marker for the selection of HfrDrd, a Hessian fly-response gene in wheat

Abstract The HfrDrd gene has been reported to be induced specifically in the wheat’s defence response to Hessian fly larvae and is not a general stress-responsive gene. The gene is located on chromosome 7DS with a homeologue on 7AS. In this study, two SNPs in the gene that result in amino acid substitutions in the dirigent-like protein have been identified. Both are C/T polymorphisms at nt position 86 and 143 in exon 1 of the gene. The first SNP (from 5′ end) causes an alanine-to-valine substitution. The second is a serine-to-leucine change and is located in the conserved dirigent domain. Both ‘T’ nucleotide SNPs are characteristic of the Hessian fly-resistant genotype, Iris (JX501668, JX501669). Only SNP 143 has been found to be significantly associated with Hessian fly resistance. One hundred and seventy-one Australian cultivars screened were susceptible and have the ‘C’ nucleotide at SNP 143. The ‘T’ SNP at nt 143 was found in thirteen resistant cultivars, and the heterozygous state was identified in four other resistant cultivars. This study has identified other resistant genotypes which do not carry the ‘T’ nucleotide at nt 143 in the gene. Their resistance mechanism possibly involves other Hessian fly-response (Hfr) genes. SNP 143 will be useful for deployment in developing varieties with the resistant HfrDrd allele.

An EST-SSR Marker Tightly Linked to the Barley Male Sterility Gene (msg6) Located on Chromosome 6H

The barley male sterility gene (msg6) located on chromosome 6H has been used in breeding and research since its discovery 7 decades ago, but to date, no research has been reported that linked the gene with molecular markers. The main objective of this study was to identify expressed sequence tag-simple sequence repeat (EST-SSR) markers linked to msg6 as this could provide opportunities for gene discovery. In a cross of a male sterile line (04-042B) with a fully fertile line (VB0330; VB9524/Mundah), male sterility segregated in a 3:1 ratio of fertile to completely sterile plants (χ(2) = 0.03, P(0.05) = 0.95), in a population of 250 F(2) plants. Multipoint linkage mapping placed the msg6 gene at 4.9 cM from the EST-SSR, GBM1267, whereas 2-point analysis estimated a recombination fraction of 0.05 ± 0.02 (logarithm of the odds score = 26.34) between the EST-SSR and the male sterility gene. Multiple interval quantitative trait locus (QTL) analysis of spike weight, an indicative measure of reproductive success, identified a QTL near GBM1267 as having a major influence, explaining 68.7% of the variation in weight of individual spikes. The GBM1267 marker segregated in a 1:2:1 ratio, which makes it highly desirable for marker-assisted selection, as it can distinguish the recessive from the dominant and from heterozygous individuals. Another EST-SSR marker, designated VBMS103, was developed in the present study to provide an additional marker with known sequence (AL501881) close to the msg6 gene. The results provide highly informative functional tools for tracking the msg6 gene in breeding programs.

Association of KASP markers with Hessian fly resistance in wheat of diverse origin

Hessian fly (Mayetiola destructor (Say)) is a major pest in wheat producing areas of United States, Canada, Europe, and North Africa but has not been found in Australia. Host plant resistance is thought to involve a similar strategy used against plant pathogen, and in this study, we sought to investigate whether disease-resistance gene markers can also be useful in selecting against Hessian fly attack. The genome-wide association study involved 251 wheat genotypes of diverse origin and 72 SNPs, selected on the basis of significant similarity of their associated contig sequences to putative disease resistance genes. A novel statistical approach for genome-wide scan was applied, which utilised genotype data scored as Null alleles in the mixed model, instead of deleting or treating them as missing alleles. The analyses identified four markers with significant associations at the 5% level, after applying the false discovery rate. These were located on chromosomes 4A, 4B, 5A and 7D, with the 5A locus mapping to the cluster of major genes that confer resistance to multiple Hessian fly biotypes. Amongst the diverse wheat accessions analysed, most of the susceptible phenotypes carried the A–G–C–C haplotype at the BS00064369, BS00007416, BS00077047 and HfrDrd_nt_143 loci, respectively. When heterozygotes were excluded, all the Australian wheat accessions carried this allelic combination. The combination of alleles conferring resistance depended on the origin of the wheat accessions, with ICARDA accessions carrying a preponderance of the C–C–CG–T. Of the 11 USA accessions used for this study, only Lola carried a favourable combination of alleles for resistance at these loci.

Field-based screening identifies resistance to Sunn pest (Eurygaster integriceps) feeding at vegetative stage in elite wheat genotypes

Abstract. Sunn pest (Eurygaster integriceps Puton) is currently widely distributed in West and Central Asia and Eastern Europe, but has not been found in Australia, Western Europe or North America. Climate warming is known to promote the expansion of its range of distribution, and it is expected that the insect could spread into new territories. Varieties of wheat (Triticum aestivum) carrying resistance remain an important component of managing the biosecurity risk of any potential incursion. Previous studies have identified sources of Sunn pest resistance in wheat, but there is little information on the genes that confer the resistance. This research used field-based, artificial infestation cages to evaluate 204 elite wheat varieties for Sunn pest resistance, at Terbol, Lebanon. A significant (P < 0.001) difference in resistance was observed among the wheat germplasm, with 19 varieties rated as resistant to moderately resistant and 17 as highly susceptible. Three of the elite varieties showed very little damage, a status similar to that of the resistant check, ICBW-209273. In parallel, the research carried out a genome-wide scan with single-nucleotide polymorphism (SNP) markers to identify chromosome regions and putative genes associated with resistance. Association mapping identified SNP markers with significant associations on chromosomes 2D, 4B and 5B. When these markers were projected onto the wheat population sequencing-based (POPSEQ) reference map, they tended to map close to the location of wheat height-reducing genes. The phenotypic variation explained by the identified markers ranged from 7% to 11%, and collectively, they explained 23.9% of the variation or 45% of the generalised heritability. Marker-trait association was confirmed in two independent, doubled-haploid wheat populations, derived from crosses involving wheat landraces from Afghanistan, where Sunn pest is recognised as an endemic problem. In the two wheat populations, the analyses validated the strong association between wsnp_BF483640B_Ta_2_2 and resistance to Sunn pest damage at the vegetative stage. This study demonstrates existence of genetic resistance to Sunn pest feeding at the vegetative stage in elite wheat germplasm. The study also identified and validated SNP markers that could be useful tools for transfer of resistance into new wheat cultivars.