DAWN: a resource for yielding insights into the diversity among wheat genomes

Identifying and Characterizing Candidate Genes Contributing to a Grain Yield QTL in Wheat

The current study focuses on identifying the candidate genes of a grain yield QTL from a double haploid population, Westonia × Kauz. The QTL region spans 20 Mbp on the IWGSC whole-genome sequence flank with 90K SNP markers. The IWGSC gene annotation revealed 16 high-confidence genes and 41 low-confidence genes. Bioinformatic approaches, including functional gene annotation, ontology investigation, pathway exploration, and gene network study using publicly available gene expression data, enabled the short-listing of four genes for further confirmation. Complete sequencing of those four genes demonstrated that only two genes are polymorphic between the parental cultivars, which are the ferredoxin-like protein gene and the tetratricopeptide-repeat (TPR) protein gene. The two genes were selected for downstream investigation. Two SNP variations were observed in the exon for both genes, with one SNP resulting in changes in amino acid sequence. qPCR-based gene expression showed that both genes were highly expressed in the high-yielding double haploid lines along with the parental cultivar Westonia. In contrast, their expression was significantly lower in the low-yielding lines in the other parent. It can be concluded that these two genes are the contributing genes to the grain yield QTL.

Multi-donor × elite-based populations reveal QTL for low-lodging wheat

Low-lodging high-yielding wheat germplasm and SNP-tagged novel alleles for lodging were identified in a process that involved selecting donors through functional phenotyping for underlying traits with a designed phenotypic screen, and a crossing strategy involving multiple-donor × elite populations. Lodging is a barrier to achieving high yield in wheat. As part of a study investigating the potential to breed low-lodging high-yielding wheat, populations were developed crossing four low-lodging high-yielding donors selected based on lodging related traits, with three cultivars. Lodging was evaluated in single rows in an early generation and subsequently in plots in 2 years with contrasting lodging environment. A large number of lines lodged less than their recurrent parents, and some were also higher yielding. Heritability for lodging was high, but the genetic correlation between contrasting environments was intermediate-low. Lodging genotypic rankings in single rows did not correlate well with plots. Populations from the highest lodging background were genotyped (90 K iSelect BeadChip array). Fourteen markers on nine chromosomes were associated with lodging, differing under high- versus low-lodging conditions. Of the fourteen markers, ten were found to co-locate with previously identified QTL for lodging-related traits or at homoeologous locations for previously identified lodging-related QTL, while the remaining four markers (in chromosomes 2D, 4D, 7B and 7D) appear to map to novel QTL for lodging. Lines with more favourable markers lodged less, suggesting value in these markers as a selection tool. This study demonstrates that the combination of donor functional phenotyping, screen design and crossing strategy can help identify novel alleles in germplasm without requiring extensive bi-parental populations.

Integrating Wheat Nucleolus Structure and Function: Variation in the Wheat Ribosomal RNA and Protein Genes

We review the coordinated production and integration of the RNA (ribosomal RNA, rRNA) and protein (ribosomal protein, RP) components of wheat cytoplasmic ribosomes in response to changes in genetic constitution, biotic and abiotic stresses. The components examined are highly conserved and identified with reference to model systems such as human, Arabidopsis, and rice, but have sufficient levels of differences in their DNA and amino acid sequences to form fingerprints or gene haplotypes that provide new markers to associate with phenotype variation. Specifically, it is argued that populations of ribosomes within a cell can comprise distinct complements of rRNA and RPs to form units with unique functionalities. The unique functionalities of ribosome populations within a cell can become central in situations of stress where they may preferentially translate mRNAs coding for proteins better suited to contributing to survival of the cell. In model systems where this concept has been developed, the engagement of initiation factors and elongation factors to account for variation in the translation machinery of the cell in response to stresses provided the precedents. The polyploid nature of wheat adds extra variation at each step of the synthesis and assembly of the rRNAs and RPs which can, as a result, potentially enhance its response to changing environments and disease threats.

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.

The effects of crop attributes, selection, and recombination on Canadian bread wheat molecular variation

Cultivated germplasm provides an opportunity to investigate how crop agronomic traits, selection for major genes, and differences in crossing-over rates drive patterns of allelic variation. To identify how these factors correlated with allelic variation within a collection of cultivated bread wheat (Triticum aestivum L.), we generated genotypes for 388 accessions grown in Canada over the past 170 yr using filtered single nucleotide polymorphism (SNP) calls from an Illumina Wheat iSelect 90K SNP-array. Entries' breeding program, era of release, grain texture, kernel color, and growth habit contributed to allelic differentiation. Allelic diversity and linkage disequilibrium (LD) of markers flanking some major loci known to affect traits such as gluten strength, growth habit, and grain color were consistent with selective sweeps. Nonetheless, some flanking markers of major loci had low LD and high allelic diversity. Positive selection may have acted upon homoeologous genes that had significant enrichment for the gene ontology terms 'response-to-auxin' and 'response-to-wounding.' Long regions of LD, spanning approximately one-third the length of entire chromosomes, were associated with many pericentromeric regions. These regions were also characterized by low diversity. Enhancing recombination across these regions could generate novel allele combinations to accelerate Canadian wheat improvement.

The wheat Seven in absentia gene is associated with increases in biomass and yield in hot climates

Wheat (Triticum aestivum L.) productivity is severely reduced by high temperatures. Breeding of heat-tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits when high temperatures occur and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We advanced the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene, Seven in absentia, TaSINA. This was associated with the QTL's effects on early vigour, root growth, plant biomass, and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL underexpressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number, and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.

The WtmsDW Locus on Wheat Chromosome 2B Controls Major Natural Variation for Floret Sterility Responses to Heat Stress at Booting Stage

Heat stress at booting stage causes significant losses to floret fertility (grain set) and hence yield in wheat (Triticum aestivum L.); however, there is a lack of well-characterized sources of tolerance to this type of stress. Here, we describe the genetic analysis of booting stage heat tolerance in a cross between the Australian cultivars Drysdale (intolerant) and Waagan (tolerant), leading to the definition of a major-effect tolerance locus on the short arm of chromosome 2B, Wheat thermosensitive male sterile Drysdale/Waagan (WtmsDW). WtmsDW offsets between 44 and 65% of the losses in grain set due to heat, suggesting that it offers significant value for marker-assisted tolerance breeding. In lines lacking the WtmsDW tolerance allele, peaks in sensitivity were defined with reference to auricle distance, for various floret positions along the spike. Other (relatively minor) floret fertility response effects, including at the Rht-D1 dwarfing locus, were considered likely escape artifacts, due to their association with height and flowering time effects that might interfere with correct staging of stems for heat treatment. Heat stress increased grain set at distal floret positions in spikelets located at the top of the spike and increased the size of spikelets at the base of the spike, but these effects were offset by greater reductions in grain set at other floret positions. Potentially orthologous loci on chromosomes 1A and 1B were identified for heat response of flowering time. The potential significance of these findings for tolerance breeding and further tolerance screening is discussed.

The WtmsDW Locus on Wheat Chromosome 2B Controls Major Natural Variation for Floret Sterility Responses to Heat Stress at Booting Stage

Heat stress at booting stage causes significant losses to floret fertility (grain set) and hence yield in wheat (Triticum aestivum L.); however, there is a lack of well-characterized sources of tolerance to this type of stress. Here, we describe the genetic analysis of booting stage heat tolerance in a cross between the Australian cultivars Drysdale (intolerant) and Waagan (tolerant), leading to the definition of a major-effect tolerance locus on the short arm of chromosome 2B, Wheat thermosensitive male sterile Drysdale/Waagan (WtmsDW). WtmsDW offsets between 44 and 65% of the losses in grain set due to heat, suggesting that it offers significant value for marker-assisted tolerance breeding. In lines lacking the WtmsDW tolerance allele, peaks in sensitivity were defined with reference to auricle distance, for various floret positions along the spike. Other (relatively minor) floret fertility response effects, including at the Rht-D1 dwarfing locus, were considered likely escape artifacts, due to their association with height and flowering time effects that might interfere with correct staging of stems for heat treatment. Heat stress increased grain set at distal floret positions in spikelets located at the top of the spike and increased the size of spikelets at the base of the spike, but these effects were offset by greater reductions in grain set at other floret positions. Potentially orthologous loci on chromosomes 1A and 1B were identified for heat response of flowering time. The potential significance of these findings for tolerance breeding and further tolerance screening is discussed.

A Major Locus on Wheat Chromosome 7B Associated With Late-Maturity α-Amylase Encodes a Putative ent-Copalyl Diphosphate Synthase

Many wheat varieties have the potential to develop unacceptably high levels of α-amylase in the grains if exposed to a cool temperature shock or simply cool temperature during the early to middle stages of grain filling. This phenomenon is referred to as late maturity α-amylase (LMA). The enzyme persists in the grain until harvest and may result in wheat with a low Falling Number that does not meet receival and export specifications. Resistance to LMA is therefore a valuable target for wheat breeders and wheat industries in general. Genetic evidence implicating a locus on the long arm of chromosome 7B in variation in LMA phenotype was confirmed in this investigation. Through intensive fine-mapping an ent-copalyl diphosphate synthase (CPS), hitherto named LMA-1, was identified as the likely candidate gene associated with variation in LMA phenotype. Single Nucleotide Polymorphisms (SNPs) within the LMA-1 coding sequence of Chinese Spring, Maringa and Halberd result in either prematurely terminated or functionally altered proteins that are associated with useful levels of resistance to LMA. LMA-1 transcripts detected in de-embryonated grain tissue from around 15 days after anthesis, several days before the synthesis of α-amylase, were low in the resistant varieties Chinese Spring and Maringa compared with LMA susceptible genotype Spica. This was associated with a dramatic reduction in the concentrations of intermediates in the gibberellin biosynthesis pathway such as GA₁₉, evidence that LMA-1 was functioning as CPS in the gibberellin biosynthesis pathway. A survey of a large collection of Australian and international wheat varieties distinguished 9 major haplotypes at the LMA-1 locus. Generally, within classes, there was notable variation for LMA phenotype and evidence for genotypes whose resistance is presumed to be due to genetic loci located elsewhere on the wheat genome. Further investigation is required to characterize the sequence of steps between LMA-1 and α-amylase synthesis as well as to gain a better understanding of the role and potential impact of other genetic loci. Diagnostic markers for sources of resistance and SNP variation reported in this study should assist breeders to deploy resistance associated with LMA-1 variants in breeding programs.

Ph2 encodes the mismatch repair protein MSH7-3D that inhibits wheat homoeologous recombination

Meiotic recombination is a critical process for plant breeding, as it creates novel allele combinations that can be exploited for crop improvement. In wheat, a complex allohexaploid that has a diploid-like behaviour, meiotic recombination between homoeologous or alien chromosomes is suppressed through the action of several loci. Here, we report positional cloning of Pairing homoeologous 2 (Ph2) and functional validation of the wheat DNA mismatch repair protein MSH7-3D as a key inhibitor of homoeologous recombination, thus solving a half-century-old question. Similar to ph2 mutant phenotype, we show that mutating MSH7-3D induces a substantial increase in homoeologous recombination (up to 5.5 fold) in wheat-wild relative hybrids, which is also associated with a reduction in homologous recombination. These data reveal a role for MSH7-3D in meiotic stabilisation of allopolyploidy and provides an opportunity to improve wheat's genetic diversity through alien gene introgression, a major bottleneck facing crop improvement.

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.

Multiple wheat genomes reveal global variation in modern breeding

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome¹, and the lack of genome-assembly data for multiple wheat lines^2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses^4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1⁶, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Comparison of multiple genome assemblies from wheat reveals extensive diversity that results from the complex breeding history of wheat and provides a basis for further potential improvements to this important food crop.

QTL analysis and fine mapping of a QTL for yield-related traits in wheat grown in dry and hot environments

Genetic control of grain yield and phenology was examined in the Excalibur/Kukri doubled haploid mapping population grown in 32 field experiments across the climatic zones of southern Australia, India and north-western Mexico where the wheat crop experiences drought and heat stress. A total of 128 QTL were identified for four traits: grain yield, thousand grain weight (TGW), days to heading and grain filling duration. These QTL included 24 QTL for yield and 27 for TGW, showing significant interactions with the environment (Q * E). We also identified 14 QTL with a significant, small main effects on yield across environments. The study focussed on a region of chromosome 1B where two main effect QTL were found for yield and TGW without the confounding effect of phenology. Excalibur was the source of favourable alleles: QYld.aww-1B.2 with a peak at 149.5-150.1 cM and QTgw.aww-1B at 168.5-171.4 cM. We developed near isogenic lines (NIL) for the interval including QYld.aww-1B.2 and QTgw.aww-1B and evaluated them under semi-controlled conditions. Significant differences in four pairs of NIL were observed for grain yield but not for TGW, confirming a positive effect of the Excalibur allele for QYld.aww-1B.2. The interval containing QYld.aww-1B.2 was narrowed down to 2.9 cM which corresponded to a 2.2 Mbp genomic region on the chromosome 1B genomic reference sequence of cv. Chinese Spring and contained 39 predicted genes.

High-resolution mapping of rachis nodes per rachis, a critical determinant of grain yield components in wheat

Exploring large genomic data sets based on the latest reference genome assembly identifies the rice ortholog APO1 as a key candidate gene for number of rachis nodes per spike in wheat. Increasing grain yield in wheat is a key breeding objective worldwide. Several component traits contribute to grain yield with spike attributes being among the most important. In this study, we performed a genome-wide association analysis for 12 grain yield and component traits measured in field trials with contrasting agrochemical input levels in a panel of 220 hexaploid winter wheats. A highly significant, environmentally consistent QTL was detected for number of rachis nodes per rachis (NRN) on chromosome 7AL. The five most significant SNPs formed a strong linkage disequilibrium (LD) block and tagged a 2.23 Mb region. Using pairwise LD for exome SNPs located across this interval in a large worldwide hexaploid wheat collection, we reduced the genomic region for NRN to a 258 Kb interval containing four of the original SNP and six high-confidence genes. The ortholog of one (TraesCS7A01G481600) of these genes in rice was ABBERANT PANICLE ORGANIZATION1 (APO1), which is known to have significant effects on panicle attributes. The APO1 ortholog was the best candidate for NRN and was associated with a 115 bp promoter deletion and two amino acid (C47F and D384 N) changes. Using a large worldwide collection of tetraploid and hexaploid wheat, we found 12 haplotypes for the NRN QTL and evidence for positive enrichment of two haplotypes in modern germplasm. Comparison of five QTL haplotypes in Australian yield trials revealed their relative, context-dependent contribution to grain yield. Our study provides diagnostic SNPs and value propositions to support deployment of the NRN trait in wheat breeding.

Genetic Dissection of Resistance to the Three Fungal Plant Pathogens Blumeria graminis, Zymoseptoria tritici, and Pyrenophora tritici-repentis Using a Multiparental Winter Wheat Population

Bread wheat (Triticum aestivum L.) is one of the world’s most important crop species. The development of new varieties resistant to multiple pathogens is an ongoing task in wheat breeding, especially in times of increasing demand for sustainable agricultural practices. Despite this, little is known about the relations between various fungal disease resistances at the genetic level, and the possible consequences for wheat breeding strategies. As a first step to fill this gap, we analyzed the genetic relations of resistance to the three fungal diseases – powdery mildew (PM), septoria tritici blotch (STB), and tan spot (TS) – using a winter wheat multiparent advanced generation intercross population. Six, seven, and nine QTL for resistance to PM, STB, and TS, respectively, were genetically mapped. Additionally, 15 QTL were identified for the three agro-morphological traits plant height, ear emergence time, and leaf angle distribution. Our results suggest that resistance to STB and TS on chromosome 2B is conferred by the same genetic region. Furthermore, we identified two genetic regions on chromosome 1AS and 7AL, which are associated with all three diseases, but not always in a synchronal manner. Based on our results, we conclude that parallel marker-assisted breeding for resistance to the fungal diseases PM, STB, and TS appears feasible. Knowledge of the genetic co-localization of alleles with contrasting effects for different diseases, such as on chromosome 7AL, allows the trade-offs of selection of these regions to be better understood, and ultimately determined at the genic level.

Genome-wide association mapping of grain yield in a diverse collection of spring wheat (Triticum aestivum L.) evaluated in southern Australia

Wheat landraces, wild relatives and other 'exotic' accessions are important sources of new favorable alleles. The use of those exotic alleles is facilitated by having access to information on the association of specific genomic regions with desirable traits. Here, we conducted a genome-wide association study (GWAS) using a wheat panel that includes landraces, synthetic hexaploids and other exotic wheat accessions to identify loci that contribute to increases in grain yield in southern Australia. The 568 accessions were grown in the field during the 2014 and 2015 seasons and measured for plant height, maturity, spike length, spike number, grain yield, plant biomass, HI and TGW. We used the 90K SNP array and two GWAS approaches (GAPIT and QTCAT) to identify loci associated with the different traits. We identified 17 loci with GAPIT and 25 with QTCAT. Ten of these loci were associated with known genes that are routinely employed in marker assisted selection such as Ppd-D1 for maturity and Rht-D1 for plant height and seven of those were detected with both methods. We identified one locus for yield per se in 2014 on chromosome 6B with QTCAT and three in 2015, on chromosomes 4B and 5A with GAPIT and 6B with QTCAT. The 6B loci corresponded to the same region in both years. The favorable haplotypes for yield at the 5A and 6B loci are widespread in Australian accessions with 112 out of 153 carrying the favorable haplotype at the 5A locus and 136 out of 146 carrying the favorable haplotype at the 6A locus, while the favorable haplotype at 4B is only present in 65 out of 149 Australian accessions. The low number of yield QTL in our study corroborate with other GWAS for yield in wheat, where most of the identified loci have very small effects.

Novel Alleles for Combined Drought and Heat Stress Tolerance in Wheat

Drought and heat waves commonly co-occur in many wheat-growing regions causing significant crop losses. The identification of stress associated quantitative trait loci, particularly those for yield, is problematic due to their association with plant phenology and the high genetic × environment interaction. Here we studied a panel of 315 diverse, spring type accessions of bread wheat (Triticum aestivum) in pots in a semi-controlled environment under combined drought and heat stress over 2 years. Importantly, we treated individual plants according to their flowering time. We found 134 out of the 145 identified loci for grain weight that were not associated with either plant phenology or plant height. The majority of loci uncovered here were novel, with favorable alleles widespread in Asian and African landraces providing opportunities for their incorporation into modern varieties through breeding. Using residual heterozygosity in lines from a nested association mapping population, we were able to rapidly develop near-isogenic lines for important target loci. One target locus on chromosome 6A contributed to higher grain weight, harvest index, thousand kernel weight, and grain number under drought and heat stress in field conditions consistent with allelic effects demonstrated in the genome-wide association study.