Elucidation of the genetic basis of variation for stem strength characteristics in bread wheat by Associative Transcriptomics

Identification and estimation of lodging in bread wheat genotypes using machine learning predictive algorithms

BACKGROUND

Lodging or stem bending decreases wheat yield quality and quantity. Thus, the traits reflected in early lodging wheat are helpful for early monitoring to some extent. In order to identify the superior genotypes and compare multiple linear regression (MLR) with support vector regression (SVR), artificial neural network (ANN), and random forest regression (RF) for predicting lodging in Iranian wheat accessions, a total of 228 wheat accessions were cultivated under field conditions in an alpha-lattice experiment, randomized incomplete block design, with two replications in two cropping seasons (2018-2019 and 2019-2020). To measure traits, a total of 20 plants were isolated from each plot and were measured using image processing.

RESULTS

The lodging score index (LS) had the highest positive correlation with plant height (r = 0.78**), Number of nodes (r = 0.71**), and internode length 1 (r = 0.70**). Genotypes were classified into four groups based on heat map output. The most lodging-resistant genotypes showed a lodging index of zero or close to zero. The findings revealed that the RF algorithm provided a more accurate estimate (R2 = 0.887 and RMSE = 0.091 for training data and R2 = 0.768 and RMSE = 0.124 for testing data) of wheat lodging than the ANN and SVR algorithms, and its robustness was as good as ANN but better than SVR.

CONCLUSION

Overall, it seems that the RF model can provide a helpful predictive and exploratory tool to estimate wheat lodging in the field. This work can contribute to the adoption of managerial approaches for precise and non-destructive monitoring of lodging.

Identification of the Solid Stem Suppressor Gene Su-TdDof in Synthetic Hexaploid Wheat Syn-SAU-117

Lodging is one of the most important factors affecting the high and stable yield of wheat worldwide. Solid-stemmed wheat has higher stem strength and lodging resistance than hollow-stemmed wheat does. There are many solid-stemmed varieties, landraces, and old varieties of durum wheat. However, the transfer of solid stem genes from durum wheat is suppressed by a suppressor gene located on chromosome 3D in common wheat, and only hollow-stemmed lines have been created. However, synthetic hexaploid wheat can serve as a bridge for transferring solid stem genes from tetraploid wheat to common wheat. In this study, the F1, F2, and F2:3 generations of a cross between solid-stemmed Syn-SAU-119 and semisolid-stemmed Syn-SAU-117 were developed. A single dominant gene, which was tentatively designated Su-TdDof and suppresses stem solidity, was identified in synthetic hexaploid wheat Syn-SAU-117 by using genetic analysis. By using bulked segregant RNA-seq (BSR-seq) analysis, Su-TdDof was mapped to chromosome 7DS and flanked by markers KASP-669 and KASP-1055 within a 4.53 cM genetic interval corresponding to 3.86 Mb and 2.29 Mb physical regions in the Chinese Spring (IWGSC RefSeq v1.1) and Ae. tauschii (AL8/78 v4.0) genomes, respectively, in which three genes related to solid stem development were annotated. Su-TdDof differed from a previously reported solid stem suppressor gene based on its origin and position. Su-TdDof would provide a valuable example for research on the suppression phenomenon. The flanking markers developed in this study might be useful for screening Ae. tauschii accessions with no suppressor gene (Su-TdDof) to develop more synthetic hexaploid wheat lines for the breeding of lodging resistance in wheat and further cloning the suppressor gene Su-TdDof.

Effect of the pectin contents and nanostructure on the stem straightness of two Paeonia lactiflora cultivars

Herbaceous peony (Paeonia lactiflora Pall.) is an ancient ornamental crop and, in recent decades, an emerging popular cut flower. Straight stems are a vital criterion for cut herbaceous peony selection, while many cultivars bend as the plant develops. Pectin helps maintain the mechanical strength of the cell wall. However, little is known about its role in the stem bending of herbaceous peony. Two herbaceous peony cultivars with contrasting stem morphologies ('Dong Fang Shao Nv', upright; 'Lan Tian Piao Xiang', bending gradually) at five developmental stages were used as materials to investigate the effects of pectin content and nanostructure on straightness using the carbazole colorimetric method and atomic force microscopy observations. The contents of water-soluble pectin (WSP), CDTA-soluble pectin (CSP), and sodium carbonate-soluble pectin (SSP) differed significantly between the two cultivars, and the contents and angle of the flower and branch showed correlations. For the pectin nanostructure, WSP showed agglomerates and long chains, with a higher proportion of broad agglomerates at the later stages of the bending cultivar than the upright cultivar. CSP showed branched chains, and the proportion of broad chains was higher in the upright cultivar at later stages, while CSP shape changed from agglomerates to chains in the bending cultivar. SSP mainly consisted of short linear main chains, and side chains in the upright stem were stacked, and the bent cultivar had more broad and short chains. It can be concluded that the contents, nanometric shape, and size of the three kinds of pectin are highly likely to affect herbaceous peony stem straightness. This study provides a theoretical basis for the role of pectin in the production and breeding of herbaceous peony cut flowers.

Development and identification of four new synthetic hexaploid wheat lines with solid stems

Stem solidness is an important agronomic trait for increasing the ability of wheat to resist lodging. In this study, four new synthetic hexaploid wheat with solid stems were developed from natural chromosome doubling of F₁ hybrids between a solid-stemmed durum wheat (Triticum turgidum ssp. durum, 2n = 4x = 28, AABB) and four Aegilops tauschii (2n = 2x = 14, DD) accessions. The solid expression of the second internode at the base of the stem was stable for two synthetic hexalpoid wheat Syn-SAU-117 and Syn-SAU-119 grown in both the greenhouse and field. The lodging resistance of four synthetic solid-stem wheats is stronger than that of CS, and Syn-SAU-116 has the strongest lodging resistance, followed by Syn-SAU-119. The paraffin sections of the second internode showed that four synthetic wheat lines had large outer diameters, well-developed mechanical tissues, large number of vascular bundles, and similar anatomical characteristics with solid-stemmed durum wheat. The chromosomal composition of four synthetic hexaploid wheat was identified by FISH (fluorescence in situ hybridization) using Oligo-pSc119.2-1 and Oligo-pTa535-1. At adult stage, all four synthetic hexaploid wheat showed high resistance to mixed physiological races of stripe rust pathogen (CYR31, CYR32, CYR33, CYR34). These synthetic hexaploid wheat lines provide new materials for the improvement of common wheat.

A transcriptome-based association study of growth, wood quality, and oleoresin traits in a slash pine breeding population

Slash pine (Pinus elliottii Engelm.) is an important timber and resin species in the United States, China, Brazil and other countries. Understanding the genetic basis of these traits will accelerate its breeding progress. We carried out a genome-wide association study (GWAS), transcriptome-wide association study (TWAS) and weighted gene co-expression network analysis (WGCNA) for growth, wood quality, and oleoresin traits using 240 unrelated individuals from a Chinese slash pine breeding population. We developed high quality 53,229 single nucleotide polymorphisms (SNPs). Our analysis reveals three main results: (1) the Chinese breeding population can be divided into three genetic groups with a mean inbreeding coefficient of 0.137; (2) 32 SNPs significantly were associated with growth and oleoresin traits, accounting for the phenotypic variance ranging from 12.3% to 21.8% and from 10.6% to 16.7%, respectively; and (3) six genes encoding PeTLP, PeAP2/ERF, PePUP9, PeSLP, PeHSP, and PeOCT1 proteins were identified and validated by quantitative real time polymerase chain reaction for their association with growth and oleoresin traits. These results could be useful for tree breeding and functional studies in advanced slash pine breeding program.

Slash pine is an important source of original timber and resin production on commercial forest plantations. It is necessary to implement precise breeding strategies to improve timber quality and resin yield. However, little is known about the species’ molecular genetic basis. Using a transcriptome dataset with sequencing from 240 individuals in the slash pine population, we combined multiple approaches (based on gene variation, expression variation and co-expression network) to dissect the genetic structure for slash pine major breeding traits. We found that the research population could be divided into three genetic groups with a mean heterozygosity of 0.2246. We also found that six genes with important functions in slash pine resin synthesis and timber formation through association studies. Four new SNPs associatation with the average ring width were also discovered. Our results provide new insights into the molecular genetic basis of important traits in slash pine and provide a comprehensive method for association analyses of conifer tree species with large genome.

QTL Identification for Stem Fiber, Strength and Rot Resistance in a DH Population from an Alien Introgression of Brassica napus

Stem fiber, stem strength and stem-rot resistance are important agronomic traits in Brassica napus. To understand the molecular mechanism that controls the stem-related traits, we investigated the stem lignin (ADL), cellulose (Cel), hemicellulose (Hem) content, S/G monolignol ratio (SG), stem breaking force (BF), breaking strength (F) and Sclerotinia sclerotiorum resistance (SSR). Each trait was significantly positively or negatively correlated with more than three of the other six traits. QTL mapping for ADL, Cel, Hem, SG, BF, F and SSR were performed using a doubled haploid population derived from an intertribal B. napus introgression line 'Y689' crossed with B. napus cv. 'Westar'. A total of 67 additive QTL were identified and integrated into 55 consensus QTL by meta-analysis. Among the 55 consensus QTL, 23 (41.8%) QTL were co-located and were integrated into 11 unique QTL. The QTL by environment (Q × E) interactions were analyzed and 22 combined QTL were identified. In addition, candidate genes within the QTL intervals were proposed based on the known function of Arabidopsis orthologs. These results provided valuable information for improving lodging resistance, S. sclerotiorum resistance and mechanized harvesting of B. napus.

Fusarium head blight resistance exacerbates nutritional loss of wheat grain at elevated CO2

The nutritional integrity of wheat is jeopardized by rapidly rising atmospheric carbon dioxide (CO₂) and the associated emergence and enhanced virulence of plant pathogens. To evaluate how disease resistance traits may impact wheat climate resilience, 15 wheat cultivars with varying levels of resistance to Fusarium Head Blight (FHB) were grown at ambient and elevated CO₂. Although all wheat cultivars had increased yield when grown at elevated CO₂, the nutritional contents of FHB moderately resistant (MR) cultivars were impacted more than susceptible cultivars_. At elevated CO₂, the MR cultivars had more significant differences in plant growth, grain protein, starch, fructan, and macro and micro-nutrient content compared with susceptible wheat. Furthermore, changes in protein, starch, phosphorus, and magnesium content were correlated with the cultivar FHB resistance rating, with more FHB resistant cultivars having greater changes in nutrient content. This is the first report of a correlation between the degree of plant pathogen resistance and grain nutritional content loss in response to elevated CO₂. Our results demonstrate the importance of identifying wheat cultivars that can maintain nutritional integrity and FHB resistance in future atmospheric CO₂ conditions.

Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil

Australian lentil production is affected by several major biotic constraints including Ascochyta blight (AB), caused by Ascochyta lentis, a devastating fungal disease. Cultivation of AB resistant cultivars, alongside agronomic management including fungicide application, is the current most economically viable control strategy. However, the breakdown of AB resistance in cultivars, such as Northfield and Nipper, suggests the need for introgression of new and diverse resistance genes. Successful introgression entails an understanding of the genetic basis of resistance. In this context, a biparental mapping population derived from a cross between a recently identified AB resistant accession ILWL 180 (Lens orientalis) and a susceptible cultivar ILL 6002 was produced. A genetic linkage map was constructed from single-nucleotide polymorphism markers generated using a genotyping-by-sequencing transcript approach. Genetic dissection of the mapping population revealed a major quantitative trait loci (QTL) region nested with three QTLs on linkage group 5 and explained 9.5-11.5 percent (%) of phenotypic variance for AB resistance. Another QTL was identified on LG2 with phenotypic variance of 9.6%. The identified QTL regions harbored putative candidate genes potentially associated with defense responses to A. lentis infection. The QTL analysis and the candidate gene information are expected to contribute to the development of diagnostic markers and enable marker-assisted resistance selection in lentil breeding programmes.

Validation of a novel associative transcriptomics pipeline in Brassica oleracea: identifying candidates for vernalisation response

BACKGROUND

Associative transcriptomics has been used extensively in Brassica napus to enable the rapid identification of markers correlated with traits of interest. However, within the important vegetable crop species, Brassica oleracea, the use of associative transcriptomics has been limited due to a lack of fixed genetic resources and the difficulties in generating material due to self-incompatibility. Within Brassica vegetables, the harvestable product can be vegetative or floral tissues and therefore synchronisation of the floral transition is an important goal for growers and breeders. Vernalisation is known to be a key determinant of the floral transition, yet how different vernalisation treatments influence flowering in B. oleracea is not well understood.

RESULTS

Here, we present results from phenotyping a diverse set of 69 B. oleracea accessions for heading and flowering traits under different environmental conditions. We developed a new associative transcriptomics pipeline, and inferred and validated a population structure, for the phenotyped accessions. A genome-wide association study identified miR172D as a candidate for the vernalisation response. Gene expression marker association identified variation in expression of BoFLC.C2 as a further candidate for vernalisation response.

CONCLUSIONS

This study describes a new pipeline for performing associative transcriptomics studies in B. oleracea. Using flowering time as an example trait, it provides insights into the genetic basis of vernalisation response in B. oleracea through associative transcriptomics and confirms its characterisation as a complex G x E trait. Candidate leads were identified in miR172D and BoFLC.C2. These results could facilitate marker-based breeding efforts to produce B. oleracea lines with more synchronous heading dates, potentially leading to improved yields.

Genome-Wide Association Analysis for Stem Cross Section Properties, Height and Heading Date in a Collection of Spanish Durum Wheat Landraces

Durum wheat landraces have a high potential for breeding but they remain underexploited due to several factors, including the insufficient evaluation of these plant materials and the lack of efficient selection tools for transferring target traits into elite backgrounds. In this work, we characterized 150 accessions of the Spanish durum wheat collection for stem cross section, height and heading date. Continuous variation and high heritabilities were recorded for the stem area, pith area, pith diameter, culm wall thickness, height and heading date. The accessions were genotyped with DArTSeq markers, which were aligned to the durum wheat 'Svevo' genome. The markers corresponding to genes, with a minor allele frequency above 5% and less than 10% of missing data, were used for genome-wide association scan analysis. Twenty-nine marker-trait associations (MTAs) were identified and compared with the positions of previously known QTLs. MTAs for height and heading date co-localized with the QTLs for these traits. In addition, all the MTAs for stem traits in chromosome 2B were located in the corresponding synteny regions of the markers associated with lodging in bread wheat. Finally, several MTAs for stem traits co-located with the QTL for wheat stem sawfly (WSS) resistance. The results presented herein reveal the same genomic regions in chromosome 2B are involved in the genetic control of stem traits and lodging tolerance in both durum and bread wheat. In addition, these results suggest the importance of stem traits for WSS resistance and the potential of these landraces as donors for lodging tolerance and WSS resistance enhancement. In this context, the MTAs for stem-related traits identified in this work can serve as a reference for further development of markers for the introgression of target traits into elite material.

Using natural variation to understand plant responses to iron availability

Iron bioavailability varies dramatically between soil types across the globe. This has given rise to high levels of natural variation in plant iron responses, allowing members of even a single species to thrive across a wide range of soil types. In recent years we have seen the use of genome-wide association analysis to identify natural variants underlying plant responses to changes in iron availability in both Arabidopsis and important crop species. These studies have provided insights into which genes have been important in shaping local adaptation to iron availability in different plant species and have allowed the discovery of novel regulators and mechanisms, not previously identified using mutagenesis approaches. Furthermore, these studies have allowed the identification of markers that can be used to accelerate breeding of future elite varieties with increased resilience to iron stress and improved nutritional quality. The studies highlighted here show that, in addition to studying plant responses to iron alone, it is important to consider these responses within the context of plant nutrition more broadly and to also consider iron regulation in relation to additional traits of agronomic importance such as yield and disease resistance.

Coevolution in Hybrid Genomes: Nuclear-Encoded Rubisco Small Subunits and Their Plastid-Targeting Translocons Accompanying Sequential Allopolyploidy Events in Triticum

The Triticum/Aegilops complex includes hybrid species resulting from homoploid hybrid speciation and allopolyploid speciation. Sequential allotetra- and allohexaploidy events presumably result in two challenges for the hybrids, which involve 1) cytonuclear stoichiometric disruptions caused by combining two diverged nuclear genomes with the maternal inheritance of the cytoplasmic organellar donor; and 2) incompatibility of chimeric protein complexes with diverged subunits from nuclear and cytoplasmic genomes. Here, we describe coevolution of nuclear rbcS genes encoding the small subunits of Rubisco (ribulose 1,5-bisphosphate carboxylase/oxygenase) and nuclear genes encoding plastid translocons, which mediate recognition and translocation of nuclear-encoded proteins into plastids, in allopolyploid wheat species. We demonstrate that intergenomic paternal-to-maternal gene conversion specifically occurred in the genic region of the homoeologous rbcS3 gene from the D-genome progenitor of wheat (abbreviated as rbcS3D) such that it encodes a maternal-like or B-subgenome-like SSU3D transit peptide in allohexaploid wheat but not in allotetraploid wheat. Divergent and limited interaction between SSU3D and the D-subgenomic TOC90D translocon subunit is implicated to underpin SSU3D targeting into the chloroplast of hexaploid wheat. This implicates early selection favoring individuals harboring optimal maternal-like organellar SSU3D targeting in hexaploid wheat. These data represent a novel dimension of cytonuclear evolution mediated by organellar targeting and transportation of nuclear proteins.

Innovative transcriptome-based genotyping highlights environmentally responsive genes for phenology, growth and yield in a non-model grain legume

The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume crop, cultivated both as a green manure and as a source of protein for animal feed and human food production. During its domestication process, numerous agronomic traits were improved, however, only two trait-related genes were identified hitherto, both by linkage mapping. Genome-wide association studies (GWAS), exploiting genomic sequencing, did not select any novel candidate gene. In the present study, an innovative method of 3'-end reduced representation transcriptomic profiling, a massive analysis of cDNA ends, has been used for genotyping of 126 L. angustifolius lines surveyed by field phenotyping. Significant genotype × environment interactions were identified for all phenology and yield traits analysed. Principal component analysis of population structure evidenced European domestication bottlenecks, visualized by clustering of breeding materials and cultivars. GWAS provided contribution towards deciphering vernalization pathway in legumes, and, apart from highlighting known domestication loci (Ku/Julius and mol), designated novel candidate genes for L. angustifolius traits. Early phenology was associated with genes from vernalization, cold-responsiveness and phosphatidylinositol signalling pathways whereas high yield with genes controlling photosynthesis performance and abiotic stress (drought or heat) tolerance. PCR-based toolbox was developed and validated to enable tracking desired alleles in marker-assisted selection. Narrow-leafed lupin was genotyped with an innovative method of transcriptome profiling and phenotyped for phenology, growth and yield traits in field. Early phenology was found associated with genes from cold-response, vernalization and phosphatidylinositol signalling pathways, whereas high yield with genes running photosystem II and drought or heat stress response. Key loci were supplied with PCR-based toolbox for marker-assisted selection.

A Brassica napus Reductase Gene Dissected by Associative Transcriptomics Enhances Plant Adaption to Freezing Stress

Cold treatment (vernalization) is required for winter crops such as rapeseed (Brassica napus L.). However, excessive exposure to low temperature (LT) in winter is also a stress for the semi-winter, early-flowering rapeseed varieties widely cultivated in China. Photosynthetic efficiency is one of the key determinants, and thus a good indicator for LT tolerance in plants. So far, the genetic basis underlying photosynthetic efficiency is poorly understood in rapeseed. Here the current study used Associative Transcriptomics to identify genetic loci controlling photosynthetic gas exchange parameters in a diversity panel comprising 123 accessions. A total of 201 significant Single Nucleotide Polymorphisms (SNPs) and 147 Gene Expression Markers (GEMs) were detected, leading to the identification of 22 candidate genes. Of these, Cab026133.1, an ortholog of the Arabidopsis gene AT2G29300.2 encoding a tropinone reductase (BnTR1), was further confirmed to be closely linked to transpiration rate. Ectopic expressing BnTR1 in Arabidopsis plants significantly increased the transpiration rate and enhanced LT tolerance under freezing conditions. Also, a much higher level of alkaloids content was observed in the transgenic Arabidopsis plants, which could help protect against LT stress. Together, the current study showed that AT is an effective approach for dissecting LT tolerance trait in rapeseed and that BnTR1 is a good target gene for the genetic improvement of LT tolerance in plant.

De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway

Gymnema sylvestre is a highly valuable medicinal plant in traditional Indian system of medicine and used in many polyherbal formulations especially in treating diabetes. However, the lack of genomic resources has impeded its research at molecular level. The present study investigated functional gene profile of G. sylvestre via RNA sequencing technology. The de novo assembly of 88.9 million high quality reads yielded 23,126 unigenes, of which 18116 were annotated against databases such as NCBI nr database, gene ontology (GO), KEGG, Pfam, CDD, PlantTFcat, UniProt & GreeNC. Total 808 unigenes mapped to 78 different Transcription Factor families, whereas 39 unigenes assigned to CYP450 and 111 unigenes coding for enzymes involved in the biosynthesis of terpenoids including transcripts for synthesis of important compounds like Vitamin E, beta-amyrin and squalene. Among them, presence of six important enzyme coding transcripts were validated using qRT-PCR, which showed high expression of enzymes involved in methyl-erythritol phosphate (MEP) pathway. This study also revealed 1428 simple sequence repeats (SSRs), which may aid in molecular breeding studies. Besides this, 8 putative long non-coding RNAs (lncRNAs) were predicted from un-annotated sequences, which may hold key role in regulation of essential biological processes in G. sylvestre. The study provides an opportunity for future functional genomic studies and to uncover functions of the lncRNAs in G. sylvestre.

Phylogenetic and population structural inference from genomic ancestry maintained in present-day common wheat Chinese landraces

Hexaploid common wheat is one of the most important food crops worldwide. Common wheat domestication began in the Fertile Crescent of the Near East approximately 10 000 years ago and then spread west into Europe and eastward into East Asia and China. However, the possible spreading route into and within China is still unclear. In this study, we successfully extracted DNA from single ancient wheat seeds and sequenced the whole genome of seven ancient samples from Xiaohe and Gumugou cemeteries in Xinjiang, China. Genomic inference and morphological observation confirmed their identity as hexaploid common wheat grown in prehistoric China at least 3200 years before present (BP). Phylogenetic and admixture analyses with RNA-seq data of modern hexaploid wheat cultivars from both China and Western countries demonstrated a close kinship of the ancient wheat to extant common wheat landraces in southwestern China. The highly similar allelic frequencies in modern landraces of the Qinghai-Tibetan plateau with the ancient wheat support the previously suggested southwestern spreading route into highland China. A subsequent dispersal route from the Qinghai-Tibetan plateau margins to the Yangtze valley was proposed in this study. Furthermore, the common wheat populations grown in the Middle and Lower Yangtze valley wheat zones were also proposed to be established by population admixture with the wheat grown in the Upper Yangtze valley. Our study reports ancient common wheat sequences at a genome-wide scale, providing important information on the origin, dispersal, and genetic improvement under cultivation of present-day wheat landraces grown in China.

High-Throughput Phenotyping Enabled Genetic Dissection of Crop Lodging in Wheat

Novel high-throughput phenotyping (HTP) approaches are needed to advance the understanding of genotype-to-phenotype and accelerate plant breeding. The first generation of HTP has examined simple spectral reflectance traits from images and sensors but is limited in advancing our understanding of crop development and architecture. Lodging is a complex trait that significantly impacts yield and quality in many crops including wheat. Conventional visual assessment methods for lodging are time-consuming, relatively low-throughput, and subjective, limiting phenotyping accuracy and population sizes in breeding and genetics studies. Here, we demonstrate the considerable power of unmanned aerial systems (UAS) or drone-based phenotyping as a high-throughput alternative to visual assessments for the complex phenological trait of lodging, which significantly impacts yield and quality in many crops including wheat. We tested and validated quantitative assessment of lodging on 2,640 wheat breeding plots over the course of 2 years using differential digital elevation models from UAS. High correlations of digital measures of lodging to visual estimates and equivalent broad-sense heritability demonstrate this approach is amenable for reproducible assessment of lodging in large breeding nurseries. Using these high-throughput measures to assess the underlying genetic architecture of lodging in wheat, we applied genome-wide association analysis and identified a key genomic region on chromosome 2A, consistent across digital and visual scores of lodging. However, these associations accounted for a very minor portion of the total phenotypic variance. We therefore investigated whole genome prediction models and found high prediction accuracies across populations and environments. This adequately accounted for the highly polygenic genetic architecture of numerous small effect loci, consistent with the previously described complex genetic architecture of lodging in wheat. Our study provides a proof-of-concept application of UAS-based phenomics that is scalable to tens-of-thousands of plots in breeding and genetic studies as will be needed to uncover the genetic factors and increase the rate of gain for complex traits in crop breeding.

High-Throughput Phenotyping Enabled Genetic Dissection of Crop Lodging in Wheat

Novel high-throughput phenotyping (HTP) approaches are needed to advance the understanding of genotype-to-phenotype and accelerate plant breeding. The first generation of HTP has examined simple spectral reflectance traits from images and sensors but is limited in advancing our understanding of crop development and architecture. Lodging is a complex trait that significantly impacts yield and quality in many crops including wheat. Conventional visual assessment methods for lodging are time-consuming, relatively low-throughput, and subjective, limiting phenotyping accuracy and population sizes in breeding and genetics studies. Here, we demonstrate the considerable power of unmanned aerial systems (UAS) or drone-based phenotyping as a high-throughput alternative to visual assessments for the complex phenological trait of lodging, which significantly impacts yield and quality in many crops including wheat. We tested and validated quantitative assessment of lodging on 2,640 wheat breeding plots over the course of 2 years using differential digital elevation models from UAS. High correlations of digital measures of lodging to visual estimates and equivalent broad-sense heritability demonstrate this approach is amenable for reproducible assessment of lodging in large breeding nurseries. Using these high-throughput measures to assess the underlying genetic architecture of lodging in wheat, we applied genome-wide association analysis and identified a key genomic region on chromosome 2A, consistent across digital and visual scores of lodging. However, these associations accounted for a very minor portion of the total phenotypic variance. We therefore investigated whole genome prediction models and found high prediction accuracies across populations and environments. This adequately accounted for the highly polygenic genetic architecture of numerous small effect loci, consistent with the previously described complex genetic architecture of lodging in wheat. Our study provides a proof-of-concept application of UAS-based phenomics that is scalable to tens-of-thousands of plots in breeding and genetic studies as will be needed to uncover the genetic factors and increase the rate of gain for complex traits in crop breeding.

A wheat caffeic acid 3-O-methyltransferase TaCOMT-3D positively contributes to both resistance to sharp eyespot disease and stem mechanical strength

Plant caffeic acid 3-O-methyltransferase (COMT) has been implicated in the lignin biosynthetic pathway through catalyzing the multi-step methylation reactions of hydroxylated monomeric lignin precursors. However, genetic evidence for its function in plant disease resistance is poor. Sharp eyespot, caused primarily by the necrotrophic fungus Rhizoctonia cerealis, is a destructive disease in hexaploid wheat (Triticum aestivum L.). In this study, a wheat COMT gene TaCOMT-3D, is identified to be in response to R. cerealis infection through microarray-based comparative transcriptomics. The TaCOMT-3D gene is localized in the long arm of the chromosome 3D. The transcriptional level of TaCOMT-3D is higher in sharp eyespot-resistant wheat lines than in susceptible wheat lines, and is significantly elevated after R. cerealis inoculation. After R. cerealis inoculation and disease scoring, TaCOMT-3D-silenced wheat plants exhibit greater susceptibility to sharp eyespot compared to unsilenced wheat plants, whereas overexpression of TaCOMT-3D enhances resistance of the transgenic wheat lines to sharp eyespot. Moreover, overexpression of TaCOMT-3D enhances the stem mechanical strength, and lignin (particular syringyl monolignol) accumulation in the transgenic wheat lines. These results suggest that TaCOMT-3D positively contributes to both wheat resistance against sharp eyespot and stem mechanical strength possibly through promoting lignin (especially syringyl monolignol) accumulation.

Genotyping-by-sequencing through transcriptomics: implementation in a range of crop species with varying reproductive habits and ploidy levels

The application of genomics in crops has the ability to significantly improve genetic gain for agriculture. Many marker-dense tools have been developed, but few have seen broad adoption in plant genomics due to issues of significant variations of genome size, levels of ploidy, single nucleotide polymorphism (SNP) frequency and reproductive habit. When combined with limited breeding activities, small research communities and scant sequence resources, the suitability of popular systems is often suboptimal and routinely fails to effectively balance cost-effectiveness and sample throughput. Genotyping-by-sequencing (GBS) encompasses a range of protocols including resequencing of the transcriptome. This study describes a skim GBS-transcriptomics (GBS-t) approach developed to be broadly applicable, cost-effective and high-throughput while still assaying a significant number of SNP loci. A range of crop species with differing levels of ploidy and degree of inbreeding/outbreeding were chosen, including perennial ryegrass, a diploid outbreeding forage grass; phalaris, a putative segmental allotetraploid outbreeding forage grass; lentil, a diploid inbreeding grain legume; and canola, an allotetraploid partially outbreeding oilseed. GBS-t was validated as a simple and largely automated, cost-effective method which generates sufficient SNPs (from 89 738 to 231 977) with acceptable levels of missing data and even genome coverage from c. 3 million sequence reads per sample. GBS-t is therefore a broadly applicable system suitable for many crops, offering advantages over other systems. The correct choice of subsequent sequence analysis software is important, and the bioinformatics process should be iterative and tailored to the specific challenges posed by ploidy variation and extent of heterozygosity.

Dissecting the complex regulation of lodging resistance in Brassica napus

Lodging continues to be a major cause of yield loss in important crop species such as Brassica napus. Understanding the genetic regulation of lodging resistance is therefore of key interest to breeders worldwide. Current strategies aimed at minimising lodging risk involve the incorporation of dwarfing genes or the application of plant growth regulators. However, despite these efforts, lodging continues to be a persistent problem and it is therefore of high interest that novel, complimentary strategies for lodging control are implemented. One approach would be to focus on understanding the genetic properties underlying stem mechanical strength. With this in mind, we screened a training genetic diversity panel of B. napus accession for variation in stem mechanical strength and related traits. Using Associative Transcriptomics, we identified molecular markers for a suite of valuable traits. Using an independent test genetic diversity panel, we show that the methods employed are robust for identification of predictive markers. Furthermore, based on conserved synteny with Arabidopsis thaliana, we are able to provide a biological context to the marker associations detected and provide evidence for a role in pectin methylesterification in contributing to stem mechanical strength in Brassicaceae.

Variation across a wheat genetic diversity panel for saccharification of hydrothermally pretreated straw

BACKGROUND

Wheat straw forms an important, reliable source of lignocellulosic biomass for use in second-generation ethanol production. However, there is limited understanding of the variation in quality of straw from current breeding cultivars, and studies on such variation have generally employed suboptimal pretreatments. There is also a degree of confusion regarding phenotypic characteristics relevant to optimising the enzymatic saccharification of cellulose after suitable pretreatments for biorefining compared with those which determine good ruminant digestibility. The aim of this study has been to (a) evaluate and compare the levels of glucose enzymatically released from straw obtained from 89 cultivars of winter wheat after optimised hydrothermal pretreatments and (b) identify the underlying phenotypic characteristics relevant to enhanced glucose production with special reference to the ratios of constituent tissue types.

RESULTS

Optimised pretreatment involved hydrothermal extraction at 210 °C for 10 min. Using excess cellulases, quantitative saccharification was achieved within 24 h. The amount of glucose released ranged from 192 to 275 mg/g. The extent of glucose release was correlated with (a) the level of internode tissue (R = 0.498; p = 6.84 × 10^-7), (b) stem height (R = 0.491; p = 1.03 × 10^-6), and (c) chemical characteristics particular to stem tissues including higher levels of cellulose (R = 0.552; p = 2.06 × 10^-8) and higher levels of lignin R = 0.494; p = 8.67 × 10^-7.

CONCLUSIONS

In order to achieve maximum yields of cellulosic glucose for second-generation ethanol production, a predisposition for wheat to produce cellulose-enriched internode stem tissue, particularly of longer length, would be beneficial. This contrasts with the ideotype for ruminant nutrition, in which an increased proportion of leaf tissue is preferable.