POTAGE: A Visualisation Tool for Speeding up Gene Discovery in Wheat

Identifying the genetic control of salinity tolerance in the bread wheat landrace Mocho de Espiga Branca

Salinity tolerance in bread wheat is frequently reported to be associated with low leaf sodium (Na+) concentrations. However, the Portuguese landrace, Mocho de Espiga Branca, accumulates significantly higher leaf Na+ but has comparable salinity tolerance to commercial bread wheat cultivars. To determine the genetic loci associated with the salinity tolerance of this landrace, an F2 mapping population was developed by crossing Mocho de Espiga Branca with the Australian cultivar Gladius. The population was phenotyped for 19 salinity tolerance subtraits using both non-destructive and destructive techniques. Genotyping was performed using genotyping-by-sequencing (GBS). Genomic regions associated with salinity tolerance were detected on chromosomes 1A, 1D, 4B and 5A for the subtraits of relative and absolute growth rate (RGR, AGR respectively), and on chromosome 2A, 2B, 4D and 5D for Na+, potassium (K+) and chloride (Cl-) accumulation. Candidate genes that encode proteins associated with salinity tolerance were identified within the loci including Na+/H+ antiporters, K+ channels, H+-ATPase, calcineurin B-like proteins (CBLs), CBL-interacting protein kinases (CIPKs), calcium dependent protein kinases (CDPKs) and calcium-transporting ATPase. This study provides a new insight into the genetic control of salinity tolerance in a Na+ accumulating bread wheat to assist with the future development of salt tolerant cultivars.

Identification of salt tolerance QTL in a wheat RIL mapping population using destructive and non-destructive phenotyping

Bread wheat (Triticum aestivum L.) is one of the most important food crops, however it is only moderately tolerant to salinity stress. To improve wheat yield under saline conditions, breeding for improved salinity tolerance of wheat is needed. We have identified nine quantitative trail loci (QTL) for different salt tolerance sub-traits in a recombinant inbred line (RIL) population, derived from the bi-parental cross of Excalibur × Kukri. This population was screened for salinity tolerance subtraits using a combination of both destructive and non-destructive phenotyping. Genotyping by sequencing (GBS) was used to construct a high-density genetic linkage map, consisting of 3236 markers, and utilised for mapping QTL. Of the nine mapped QTL, six were detected under salt stress, including QTL for maintenance of shoot growth under salinity (QG(1-5).asl-5A, QG(1-5).asl-7B) sodium accumulation (QNa.asl-2A), chloride accumulation (QCl.asl-2A, QCl.asl-3A) and potassium:sodium ratio (QK:Na.asl-2DS2). Potential candidate genes within these QTL intervals were shortlisted using bioinformatics tools. These findings are expected to facilitate the breeding of new salt tolerant wheat cultivars.

Identification of Rf9, a Gene Contributing to the Genetic Complexity of Fertility Restoration in Hybrid Wheat

Wheat (Triticum aestivum L.) is a self-pollinating crop whose hybrids offer the potential to provide a major boost in yield. Male sterility induced by the cytoplasm of Triticum timopheevii is a powerful method for hybrid seed production. Hybrids produced by this method are often partially sterile, and full fertility restoration is crucial for wheat production using hybrid cultivars. To identify the genetic loci controlling fertility restoration in wheat, we produced two cytoplasmic male-sterile (CMS) backcross (BC1) mapping populations. The restorer lines Gerek 79 and 71R1203 were used to pollinate the male-sterile winter wheat line CMS-Sperber. Seed set and numbers of sterile spikelets per spike were evaluated in 340 and 206 individuals of the populations derived from Gerek 79 and 71R1203, respectively. Genetic maps were constructed using 930 and 994 single nucleotide polymorphism (SNP) markers, spanning 2,160 and 2,328 cM over 21 linkage groups in the two populations, respectively. Twelve quantitative trait loci (QTL) controlled fertility restoration in both BC1 populations, including a novel restorer-of-fertility (Rf) locus flanked by the SNP markers IWB72413 and IWB1550 on chromosome 6AS. The locus was mapped as a qualitative trait in the BC1 Gerek 79 population and was designated Rf9. One hundred-nineteen putative candidate genes were predicted within the QTL region on chromosome 6AS. Among them were genes encoding mitochondrial transcription termination factor and pentatricopeptide repeat-containing proteins that are known to be associated with fertility restoration. This finding is a promising step to better understand the functions of genes for improving fertility restoration in hybrid wheat.

Large-scale stage-specific regulation of gene expression during host-pathogen interactions in CSP44 bread wheat carrying APR gene Lr48

Genome-wide transcriptome analysis was undertaken in a leaf-rust resistant bread wheat line CSP44 (selected from Australian cv. Condor) carrying the adult plant resistance (APR) gene Lr48. Two pre-adult plant (P-AP) susceptible stages (S48 and S96) and two adult plant (AP) resistant stages (R48 and R96) were used for RNA-seq. At the susceptible P-AP stage (during S48 to S96), expression increased in 2062 genes, and declined in 130 genes; 1775 of 2062 differentially expressed genes (DEGs) also exhibited high expression during early incompatible stage R48. Comparison of S96 with R96 showed that the expression of 80 genes was enhanced and that of 208 genes declined at the AP stage. At the resistant AP stage (during R48 to R96), expression of mere 25 genes increased and that of 126 genes declined. Apparently, the resistance during late adult stage (R96) is caused by regulation of the expression of relatively fewer genes, although at pre-adult stage (S48 to S96), expression of large number of genes increased; expression of majority of these genes kept on increasing during adult stage at R48 also. These and other results of the present study suggest that APR may mimic some kind of systemic acquired resistance (SAR). The host-specific DEGs belonged to 10 different classes including genes involved in defence, transport, epigenetics, photosynthesis, genes encoding some transcription factors etc. The pathogen (Puccinia triticina) specific DEGs (including three genes encoding known biotrophic effectors) seem to help the pathogen in infection/growth through large-scale stage-specific enhanced expression of host's genes. A putative candidate gene for Lr48 containing protein kinase domain (its ortholog in rice encoding OsWAK8) was also identified.

Map-based cloning of QFhb.mgb-2A identifies a WAK2 gene responsible for Fusarium Head Blight resistance in wheat

Fusarium graminearum is one of the most threating pathogen of wheat, responsible for Fusarium head blight (FHB) which annually leads to yield losses, grain quality decay and accumulation of harmful mycotoxins in kernels. Host resistance represents the most effective approach to limit disease damages; however, only a limited number of resistant loci have currently been detected in durum genotypes. In this work we report the map-based cloning of a FHB-QTL on 2A chromosome of durum wheat, introgressed from a resistant line derived from the Chinese wheat cv. Sumai-3. A marker enrichment of the QTL region was carried out leading to the inclusion of 27 new SNPs respect to the previous map. A wall-associated receptor-like kinase (WAK2) gene was identified in the region and sequenced, in the resistant parent (^RP) one gene was predicted accounting for a genomic sequence of 5,613 structured into 6 exons, whereas two adjacent genes were predicted on the same DNA plus strand of the susceptible parent (^SP).t The involvement of WAK2 gene in FHB resistance mechanism was assessed by gene expression comparison between resistant and susceptible wheat lines, and disease symptoms evaluation in 3 TILLING mutants for WAK protein function.

Genetic factors affecting Fusarium head blight resistance improvement from introgression of exotic Sumai 3 alleles (including Fhb1, Fhb2, and Fhb5) in hard red spring wheat

BACKGROUND

Fusarium head blight resistance genes, Fhb1 (for Type-II resistance), Fhb2 (Type-II), and Fhb5 (Type-I plus some Type-II), which originate from Sumai 3, are among the most important that confer resistance in hexaploid wheat. Near-isogenic lines (NILs), in the CDC Alsask (susceptible; n = 32) and CDC Go (moderately susceptible; n = 38) backgrounds, carrying these genes in all possible combinations were developed using flanking microsatellite markers and evaluated for their response to FHB and deoxynivalenol (DON) accumulation in eight environments. NILs were haplotyped with wheat 90 K iSelect assay to elucidate the genomic composition and confirm alleles' presence. Other than evaluating the effects of three major genes in common genetic background, the study elucidated the epistatic gene interactions as they influence FHB measurements; identified loci other than Fhb1, Fhb2, and Fhb5, in both recurrent and donor parents and examined annotated proteins in gene intervals.

RESULTS

Genotyping using 81,857 single nucleotide polymorphism (SNP) markers revealed polymorphism on all chromosomes and that the NILs carried < 3% of alleles from the resistant donor. Significant improvement in field resistance (Type-I + Type-II) resulted only among the CDC Alsask NILs, not the CDC Go NILs. The phenotypic response of NILs carrying combinations of Sumai 3 derived genes suggested non-additive responses and Fhb5 was as good as Fhb1 in conferring field resistance in both populations. In addition to Fhb1, Fhb2, and Fhb5, four to five resistance improving alleles in both populations were identified and three of five in CDC Go were contributed by the susceptible parent. The introgressed chromosome regions carried genes encoding disease resistance proteins, protein kinases, nucleotide-binding and leucine rich repeats' domains. Complex epistatic gene-gene interactions among marker loci (including Fhb1, Fhb2, Fhb5) explained > 20% of the phenotypic variation in FHB measurements.

CONCLUSIONS

Immediate Sumai 3 derivatives carry a number of resistance improving minor effect alleles, other than Fhb1, Fhb2, Fhb5. Results verified that marker-assisted selection is possible for the introgression of exotic FHB resistance genes, however, the genetic background of the recipient line and epistatic interactions can have a strong influence on expression and penetrance of any given gene.

Genetic Mapping of Resistance in Hexaploid Wheat for a Quarantine Disease: Karnal Bunt

Karnal bunt (KB) of wheat, caused by Tilletia indica, is one of the greatest challenges to grain industry, not because of yield loss, but quarantine regulations that restrict international movement and trade of affected stocks. Genetic resistance is the best way to manage this disease. Although several different sources of resistance have been identified to date, very few of those have been subjected to genetic analyses. Understanding the genetics of resistance, characterization and mapping of new resistance loci can help in development of improved germplasm. The objective of this study was to identify and characterize resistance loci (QTL) in two independent recombinant inbred lines (RILs) populations utilizing different wheat lines as resistance donors. Elite CIMMYT wheat lines Blouk#1 and Huirivis#1 were used as susceptible female parents and WHEAR/KUKUNA/3/C80.1/3∗BATAVIA//2∗WBLL1 (WKCBW) and Mutus as moderately resistant male parents in Pop1 and Pop2 populations, respectively. Populations were evaluated for KB resistance in 2015-16 and 2016-17 cropping seasons at two seeding dates (total four environments) in Cd. Obregon, Mexico. Two stable QTL from each population were identified in each environment: QKb.cim-2B and QKb.cim-3D (Pop1), QKb.cim-3B1 and QKb.cim-5B2 (Pop2). Other than those four QTL, other QTL were detected in each population which were specific to environments: QKb.cim-5B1, QKb.cim-6A, and QKb.cim-7A (Pop1), QKb.cim-3B2, QKb.cim-4A1, QKb.cim-4A2, QKb.cim-4B, QKb.cim-5A1, QKb.cim-5A2, and QKb.cim-7A2 (Pop2). Among the four stable QTL, all but QKb.cim-3B1 were derived from the resistant parent. QKb.cim-2B and QKb.cim-3D in Pop1 and QKb.cim-3B1 and QKb.cim-5B2 in Pop2 explained 5.0-11.4% and 3.3-7.1% phenotypic variance, respectively. A combination of two stable QTL in each population reduced KB infection by 24-33%, respectively. Transgressive resistant segregants lines derived with resistance alleles from both parents in each population were identified. Single nucleotide polymorphism (SNP) markers flanking these QTL regions may be amenable to marker-assisted selection. The best lines from both populations (in agronomy, end-use quality and KB resistance) carrying resistance alleles at all identified loci, may be used for inter-crossing and selection of improved germplasm in future. Markers flanking these QTL may assist in selection of such lines.

Mapping of novel salt tolerance QTL in an Excalibur × Kukri doubled haploid wheat population

KEY MESSAGE

Novel QTL for salinity tolerance traits have been detected using non-destructive and destructive phenotyping in bread wheat and were shown to be linked to improvements in yield in saline fields. Soil salinity is a major limitation to cereal production. Breeding new salt-tolerant cultivars has the potential to improve cereal crop yields. In this study, a doubled haploid bread wheat mapping population, derived from the bi-parental cross of Excalibur × Kukri, was grown in a glasshouse under control and salinity treatments and evaluated using high-throughput non-destructive imaging technology. Quantitative trait locus (QTL) analysis of this population detected multiple QTL under salt and control treatments. Of these, six QTL were detected in the salt treatment including one for maintenance of shoot growth under salinity (QG(1-5).asl-7A), one for leaf Na+ exclusion (QNa.asl-7A) and four for leaf K+ accumulation (QK.asl-2B.1, QK.asl-2B.2, QK.asl-5A and QK:Na.asl-6A). The beneficial allele for QG(1-5).asl-7A (the maintenance of shoot growth under salinity) was present in six out of 44 mainly Australian bread and durum wheat cultivars. The effect of each QTL allele on grain yield was tested in a range of salinity concentrations at three field sites across 2 years. In six out of nine field trials with different levels of salinity stress, lines with alleles for Na+ exclusion and/or K+ maintenance at three QTL (QNa.asl-7A, QK.asl-2B.2 and QK:Na.asl-6A) excluded more Na+ or accumulated more K+ compared to lines without these alleles. Importantly, the QK.asl-2B.2 allele for higher K+ accumulation was found to be associated with higher grain yield at all field sites. Several alleles at other QTL were associated with higher grain yields at selected field sites.