Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent

Form follows function in Triticeae inflorescences

Grass inflorescences produce grains, which are directly connected to our food. In grass crops, yields are mainly affected by grain number and weight; thus, understanding inflorescence shape is crucially important for cereal crop breeding. In the last two decades, several key genes controlling inflorescence shape have been elucidated, thanks to the availability of rich genetic resources and powerful genomics tools. In this review, we focus on the inflorescence architecture of Triticeae species, including the major cereal crops wheat and barley. We summarize recent advances in our understanding of the genetic basis of spike branching, and spikelet and floret development in the Triticeae. Considering our changing climate and its impacts on cereal crop yields, we also discuss the future orientation of research.

The barley mutant multiflorus2.b reveals quantitative genetic variation for new spikelet architecture

Spikelet indeterminacy and supernumerary spikelet phenotypes in barley multiflorus2.b mutant show polygenic inheritance. Genetic analysis of multiflorus2.b revealed major QTLs for spikelet determinacy and supernumerary spikelet phenotypes on 2H and 6H chromosomes. Understanding the genetic basis of yield forming factors in small grain cereals is of extreme importance, especially in the wake of stagnation of further yield gains in these crops. One such yield forming factor in these cereals is the number of grain-bearing florets produced per spikelet. Wild-type barley (Hordeum vulgare L.) spikelets are determinate structures, and the spikelet axis (rachilla) degenerates after producing single floret. In contrast, the rachilla of wheat (Triticum ssp.) spikelets, which are indeterminate, elongates to produce up to 12 florets. In our study, we characterized the barley spikelet determinacy mutant multiflorus2.b (mul2.b) that produced up to three fertile florets on elongated rachillae of lateral spikelets. Apart from the lateral spikelet indeterminacy (LS-IN), we also characterized the supernumerary spikelet phenotype in the central spikelets (CS-SS) of mul2.b. Through our phenotypic and genetic analyses, we identified two major QTLs on chromosomes 2H and 6H, and two minor QTLs on 3H for the LS-IN phenotype. For, the CS-SS phenotype, we identified one major QTL on 6H, and a minor QTL on 5H chromosomes. Notably, the 6H QTLs for CS-SS and LS-IN phenotypes co-located with each other, potentially indicating that a single genetic factor might regulate both phenotypes. Thus, our in-depth phenotyping combined with genetic analyses revealed the quantitative nature of the LS-IN and CS-SS phenotypes in mul2.b, paving the way for cloning the genes underlying these QTLs in the future.

Advances and Challenges for QTL Analysis and GWAS in the Plant-Breeding of High-Yielding: A Focus on Rapeseed

Yield is one of the most important agronomic traits for the breeding of rapeseed (Brassica napus L), but its genetic dissection for the formation of high yield remains enigmatic, given the rapid population growth. In the present review, we review the discovery of major loci underlying important agronomic traits and the recent advancement in the selection of complex traits. Further, we discuss the benchmark summary of high-throughput techniques for the high-resolution genetic breeding of rapeseed. Biparental linkage analysis and association mapping have become powerful strategies to comprehend the genetic architecture of complex agronomic traits in crops. The generation of improved crop varieties, especially rapeseed, is greatly urged to enhance yield productivity. In this sense, the whole-genome sequencing of rapeseed has become achievable to clone and identify quantitative trait loci (QTLs). Moreover, the generation of high-throughput sequencing and genotyping techniques has significantly enhanced the precision of QTL mapping and genome-wide association study (GWAS) methodologies. Furthermore, this study demonstrates the first attempt to identify novel QTLs of yield-related traits, specifically focusing on ovule number per pod (ON). We also highlight the recent breakthrough concerning single-locus-GWAS (SL-GWAS) and multi-locus GWAS (ML-GWAS), which aim to enhance the potential and robust control of GWAS for improved complex traits.

Genome-wide identification of loci modifying spike-branching in tetraploid wheat

Genetic modification of spike architecture is essential for improving wheat yield. Newly identified loci for the 'Miracle wheat' phenotype on chromosomes 1AS and 2BS have significant effects on spike traits. The wheat (Triticum ssp.) inflorescence, also known as a spike, forms an unbranched inflorescence in which the inflorescence meristem generates axillary spikelet meristems (SMs) destined to become sessile spikelets. Previously, we identified the putatively causative mutation in the branched head^t (bh^t) gene (TtBH-A1) of tetraploid wheat (T. turgidum convar. compositum (L.f.) Filat.) responsible for the loss of SM identity, converting the non-branching spike to a branched wheat spike. In the current study, we performed whole-genome quantitative trait loci (QTL) analysis using 146 recombinant inbred lines (RILs) derived from a cross between spike-branching wheat ('Miracle wheat') and an elite durum wheat cultivar showing broad phenotypic variation for spike architecture. Besides the previously found gene at the bh^t-A1 locus on the short arm of chromosome 2A, we also mapped two new modifier QTL for spike-branching on the short arm of chromosome 1A, termed bh^t-A2, and 2BS. Using biparental mapping population and GWAS in 302 diverse accessions, the 2BS locus was highly associated with coding sequence variation found at the homoeo-allele of TtBH-B1 (bh^t-B1). Thus, RILs that combined both bh^t-A1 and bh^t-B1 alleles showed additive genetic effects leading to increased penetrance and expressivity of the supernumerary spikelet and/or mini-spike formation.

Genome wide genetic dissection of wheat quality and yield related traits and their relationship with grain shape and size traits in an elite × non-adapted bread wheat cross

The genetic gain in yield and quality are two major targets of wheat breeding programs around the world. In this study, a high density genetic map consisting of 10,172 SNP markers identified a total of 43 genomic regions associated with three quality traits, three yield traits and two agronomic traits in hard red spring wheat (HRSW). When compared with six grain shape and size traits, the quality traits showed mostly independent genetic control (~18% common loci), while the yield traits showed moderate association (~53% common loci). Association of genomic regions for grain area (GA) and thousand-grain weight (TGW), with yield suggests that targeting an increase in GA may help enhancing wheat yield through an increase in TGW. Flour extraction (FE), although has a weak positive phenotypic association with grain shape and size, they do not share any common genetic loci. A major contributor to plant height was the Rht8 locus and the reduced height allele was associated with significant increase in grains per spike (GPS) and FE, and decrease in number of spikes per square meter and test weight. Stable loci were identified for almost all the traits. However, we could not find any QTL in the region of major known genes like GPC-B1, Ha, Rht-1, and Ppd-1. Epistasis also played an important role in the genetics of majority of the traits. In addition to enhancing our knowledge about the association of wheat quality and yield with grain shape and size, this study provides novel loci, genetic information and pre-breeding material (combining positive alleles from both parents) to enhance the cultivated gene pool in wheat germplasm. These resources are valuable in facilitating molecular breeding for wheat quality and yield improvement.

Genetic insights into morphometric inflorescence traits of wheat

KEY MESSAGE

Modifying morphometric inflorescence traits is important for increasing grain yield in wheat. Mapping revealed nine QTL, including new QTL and a new allele for the q locus, controlling wheat spike morphometric traits. To identify loci controlling spike morphometric traits, namely spike length (SL), internode length (IL), node number per spike (NPS), and node density (ND), we studied 146 Recombinant Inbred Lines of tetraploid wheat (Triticum turgidum L.) derived from standard spike and spike-branching mutant parents. Phenotypic analyses of spike morphometric traits showed low genetic coefficients of variation, resulting in high heritabilities. The phenotypic correlation between NPS with growing degree days (GDD) suggested the importance of GDD in the determination of node number in wheat. The major effect QTL for GDD or heading date was mapped to chromosome 7BS carrying the flowering time gene, Vrn3-B1. Mapping also identified nine QTL controlling spike morphometric traits. Most of these loci controlled more than a single trait, suggesting a close genetic interrelationship among spike morphometric traits. For example, this study identified a new QTL, QND.ipk-4AL, controlling ND (up to 17.6% of the phenotypic variance), IL (up to 11% of the phenotypic variance), and SL (up to 20.8% of the phenotypic variance). Similarly, the major effect QTL for IL was mapped to the q locus. Sequencing of the Q/q gene further revealed a new q allele, qdel-5A, in spike-branching accessions possessing a six base pair deletion close to the miR172 target site. The identification of qdel-5A suggested that the spike-branching tetraploid wheats are double mutants for the spikelet meristem (SM) identity gene, i.e., branched headt (TtBHt), and the q gene, which is believed to be involved in the SM indeterminacy complex in wheat.

Genes WHEAT FRIZZY PANICLE and SHAM RAMIFICATION 2 independently regulate differentiation of floral meristems in wheat

BACKGROUND

Inflorescences of wheat species, spikes, are characteristically unbranched and bear one sessile spikelet at a spike rachis node. Development of supernumerary spikelets (SSs) at rachis nodes or on the extended rachillas is abnormal. Various wheat morphotypes with altered spike morphology, associated with the development of SSs, present an important genetic resource for studies on genetic regulation of wheat inflorescence development.

RESULTS

Here we characterized diploid and tetraploid wheat lines of various non-standard spike morphotypes, which allowed for identification of a new mutant allele of the WHEAT FRIZZY PANICLE (WFZP) gene that determines spike branching in diploid wheat Ttiticum monococcum L. Moreover, we found that the development of SSs and spike branching in wheat T. durum Desf. was a result of a wfzp-A/TtBH-A1 mutation that originated from spontaneous hybridization with T. turgidum convar. сompositum (L.f.) Filat. Detailed characterization of the false-true ramification phenotype controlled by the recessive sham ramification 2 (shr2) gene in tetraploid wheat T. turgidum L. allowed us to suggest putative functions of the SHR2 gene that may be involved in the regulation of spikelet meristem fate and in specification of floret meristems. The results of a gene interaction test suggested that genes WFZP and SHR2 function independently in different processes during spikelet development, whereas another spike ramification gene(s) interact(s) with SHR2 and share(s) common functions.

CONCLUSIONS

SS mutants represent an important genetic tool for research on the development of the wheat spikelet and for identification of genes that control meristem activities. Further studies on different non-standard SS morphotypes and wheat lines with altered spike morphology will allow researchers to identify new genes that control meristem identity and determinacy, to elucidate the interaction between the genes, and to understand how these genes, acting in concert, regulate the development of the wheat spike.

Major genes determining yield-related traits in wheat and barley

Current development of advanced biotechnology tools allows us to characterize the role of key genes in plant productivity. The implementation of this knowledge in breeding strategies might accelerate the progress in obtaining high-yielding cultivars. The achievements of the Green Revolution were based on a specific plant ideotype, determined by a single gene involved in gibberellin signaling or metabolism. Compared with the 1950s, an enormous increase in our knowledge about the biological basis of plant productivity has opened new avenues for novel breeding strategies. The large and complex genomes of diploid barley and hexaploid wheat represent a great challenge, but they also offer a large reservoir of genes that can be targeted for breeding. We summarize examples of productivity-related genes/mutants in wheat and barley, identified or characterized by means of modern biology. The genes are classified functionally into several groups, including the following: (1) transcription factors, regulating spike development, which mainly affect grain number; (2) genes involved in metabolism or signaling of growth regulators-cytokinins, gibberellins, and brassinosteroids-which control plant architecture and in consequence stem hardiness and grain yield; (3) genes determining cell division and proliferation mainly impacting grain size; (4) floral regulators influencing inflorescence architecture and in consequence seed number; and (5) genes involved in carbohydrate metabolism having an impact on plant architecture and grain yield. The implementation of selected genes in breeding programs is discussed, considering specific genotypes, agronomic and climate conditions, and taking into account that many of the genes are members of multigene families.

Genetic architecture of male floral traits required for hybrid wheat breeding

This study revealed a complex genetic architecture of male floral traits in wheat, and Rht-D1 was identified as the only major QTL. Genome-wide prediction approaches but also phenotypic recurrent selection appear promising to increase outcrossing ability required for hybrid wheat seed production. Hybrid wheat breeding is a promising approach to increase grain yield and yield stability. However, the identification of lines with favorable male floral characteristics required for hybrid seed production currently poses a severe bottleneck for hybrid wheat breeding. This study therefore aimed to unravel the genetic architecture of floral traits and to assess the potential of genomic approaches to accelerate their improvement. To this end, we employed a panel of 209 diverse winter wheat lines assessed for male floral traits and genotyped with genome-wide markers as well as for Rht-B1 and Rht-D1. We found the highest proportion of explained genotypic variance for the Rht-D1 locus (11-24 %), for which the dwarfing allele Rht-D1b had a negative effect on anther extrusion, visual anther extrusion and pollen mass. The genome-wide scan detected only few QTL with small or medium effects, indicating a complex genetic architecture. Consequently, marker-assisted selection yielded only moderate prediction abilities (0.44-0.63), mainly relying on Rht-D1. Genomic selection based on weighted ridge-regression best linear unbiased prediction achieved higher prediction abilities of up to 0.70 for anther extrusion. In conclusion, recurrent phenotypic selection appears most cost-effective for the initial improvement of floral traits in wheat, while genome-wide prediction approaches may be worthwhile when complete marker profiles are already available in a hybrid wheat breeding program.

Radiation hybrid maps of the D-genome of Aegilops tauschii and their application in sequence assembly of large and complex plant genomes

BACKGROUND

The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay.

METHODS

In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii.

RESULTS

A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average deletion size of 42.0 Mb. A total of 520 markers were anchored to 216 Ae. tauschii sequence scaffolds, 116 of which were not anchored earlier to the D-genome.

CONCLUSION

This study reports the development of first high resolution RH maps for the D-genome of Ae. tauschii accession AL8/78, which were then used for the anchoring of unassigned sequence scaffolds. This study demonstrates how RH mapping, which offered high and uniform resolution across the length of the chromosome, can facilitate the complete sequence assembly of the large and complex plant genomes.

Genome-Wide Mapping of Spike-Related and Agronomic Traits in a Common Wheat Population Derived from a Supernumerary Spikelet Parent and an Elite Parent

In wheat, exotic genotypes harbor a broad range of spike-related traits, and can be used as a source of new genes for germplasm enhancement in wheat breeding programs. In the present study, a population of 163 recombinant inbred lines was derived from a cross between an elite line (WCB414) and an exotic line (WCB617) with branched spike (supernumerary spikelet; SS) head morphology. The population was evaluated over four to six environments to identify quantitative trait loci (QTL) associated with nine spike-related traits and 10 agronomic traits. A genetic map consisting of 939 diversity arrays technology (DArT) markers was constructed. Composite interval mapping identified a total of 143 QTL located on 17 different wheat chromosomes and included 33 consistent and definitive QTL. The amount of phenotype variation explained (PVE) by individual QTL ranged from 0.61 to 91.8%. One major QTL for glume pubescence was located in a QTL-rich region on the short arm of chromosome 1A, where loci for other traits such as for kernels per spike (KS) and spike length (SL) were also identified. Similarly, a cluster of QTL associated with yield-related, agronomic and spike-related traits contributing up to 40.3% of PVE was found on the short arm of chromosome 2D, in the vicinity of a major QTL for SS-related traits. Consistent and major QTL identified in the present study may be useful in marker-assisted breeding programs to facilitate transfer of desirable alleles into other germplasm. Desirable QTL alleles were also contributed by the exotic line, suggesting the possibility of enriching the breeding germplasm with alleles from SS genotypes.

New QTL alleles for quality-related traits in spring wheat revealed by RIL population derived from supernumerary × non-supernumerary spikelet genotypes

A population developed from an exotic line with supernumerary spikelets was genetically dissected for eight quality traits, discovering new genes/alleles with potential use in wheat breeding programs. Identifying new QTLs and alleles in exotic germplasm is paramount for further improvement of quality traits in wheat. In the present study, an RIL population developed from a cross of an elite wheat line (WCB414) and an exotic genotype with supernumerary spikelets (SS) was used to identify QTLs and new alleles for eight quality traits. Composite interval mapping for 1,000 kernels weight (TKW), kernel volume weight (KVW), grain protein content (GPC), percent of flour extraction (FE) and four mixograph-related traits identified a total of 69 QTLs including 19 stable QTLs. These QTLs were located on 18 different chromosomes (except 4D, 5D, and 6D). Thirteen of these QTLs explained more than 15% of phenotypic variation (PV) and were considered as major QTLs. In this study, we identified 11 QTLs for TKW (R (2) = 7.2-17.1 %), 10 for KVW (R (2) = 6.7-22.5%), 11 for GPC (R (2) = 4.7-16.9%), 6 for FE (R (2) = 4.8-19%) and 31 for mixograph-related traits (R (2) = 3.2-41.2%). In this population, several previously identified QTLs for SS, nine spike-related and ten agronomic traits were co-located with the quality QTLs, suggesting pleiotropic effects or close linkage among loci. The traits GPC and mixogram-related traits were positively correlated with SS. Indeed, several loci for quality traits were co-located with QTL for SS. The exotic parent contributed positive alleles that increased PV of the traits at 56% of loci demonstrating the suitability of germplasm with SS to improve quality traits in wheat.