Genomic selection for target traits in the Australian lentil breeding program

Genomic selection (GS) uses associations between markers and phenotypes to predict the breeding values of individuals. It can be applied early in the breeding cycle to reduce the cross-to-cross generation interval and thereby increase genetic gain per unit of time. The development of cost-effective, high-throughput genotyping platforms has revolutionized plant breeding programs by enabling the implementation of GS at the scale required to achieve impact. As a result, GS is becoming routine in plant breeding, even in minor crops such as pulses. Here we examined 2,081 breeding lines from Agriculture Victoria’s national lentil breeding program for a range of target traits including grain yield, ascochyta blight resistance, botrytis grey mould resistance, salinity and boron stress tolerance, 100-grain weight, seed size index and protein content. A broad range of narrow-sense heritabilities was observed across these traits (0.24-0.66). Genomic prediction models were developed based on 64,781 genome-wide SNPs using Bayesian methodology and genomic estimated breeding values (GEBVs) were calculated. Forward cross-validation was applied to examine the prediction accuracy of GS for these targeted traits. The accuracy of GEBVs was consistently higher (0.34-0.83) than BLUP estimated breeding values (EBVs) (0.22-0.54), indicating a higher expected rate of genetic gain with GS. GS-led parental selection using early generation breeding materials also resulted in higher genetic gain compared to BLUP-based selection performed using later generation breeding lines. Our results show that implementing GS in lentil breeding will fast track the development of high-yielding cultivars with increased resistance to biotic and abiotic stresses, as well as improved seed quality traits

Pulse Root Ideotype for Water Stress in Temperate Cropping System

Pulses are a key component of crop production systems in Southern Australia due to their rotational benefits and potential profit margins. However, cultivation in temperate cropping systems such as that of Southern Australia is limited by low soil water availability and subsoil constraints. This limitation of soil water is compounded by the irregular rainfall, resulting in the absence of plant available water at depth. An increase in the productivity of key pulses and expansion into environments and soil types traditionally considered marginal for their growth will require improved use of the limited soil water and adaptation to sub soil constrains. Roots serve as the interface between soil constraints and the whole plant. Changes in root system architecture (RSA) can be utilised as an adaptive strategy in achieving yield potential under limited rainfall, heterogenous distribution of resources and other soil-based constraints. The existing literature has identified a “‘Steep, Deep and Cheap” root ideotype as a preferred RSA. However, this idiotype is not efficient in a temperate system where plant available water is limited at depth. In addition, this root ideotype and other root architectural studies have focused on cereal crops, which have different structures and growth patterns to pulses due to their monocotyledonous nature and determinant growth habit. The paucity of pulse-specific root architectural studies warrants further investigations into pulse RSA, which should be combined with an examination of the existing variability of known genetic traits so as to develop strategies to alleviate production constraints through either tolerance or avoidance mechanisms. This review proposes a new model of root system architecture of “Wide, Shallow and Fine” roots based on pulse roots in temperate cropping systems. The proposed ideotype has, in addition to other root traits, a root density concentrated in the upper soil layers to capture in-season rainfall before it is lost due to evaporation. The review highlights the potential to achieve this in key pulse crops including chickpea, lentil, faba bean, field pea and lupin. Where possible, comparisons to determinate crops such as cereals have also been made. The review identifies the key root traits that have shown a degree of adaptation via tolerance or avoidance to water stress and documents the current known variability that exists in and amongst pulse crops setting priorities for future research

Automated phenotyping for early vigour of field pea seedlings in controlled environment by colour imaging technology.

Early vigour of seedlings is a beneficial trait of field pea (Pisum sativum L.) that contributes to weed control, water use efficiency and is likely to contribute to yield under certain environments. Although breeding is considered the most effective approach to improve early vigour of field pea, the absence of a robust and high-throughput phenotyping tool to dissect this complex trait is currently a major obstacle of genetic improvement programs to address this issue. To develop this tool, separate trials on 44 genetically diverse field pea genotypes were conducted in the automated plant phenotyping platform of Plant Phenomics Victoria, Horsham and in the field, respectively. High correlation between estimated plant parameters derived from the automated phenotyping platform and important early vigour traits such as shoot biomass, leaf area and plant height indicated that the derived plant parameters can be used to predict vigour traits in field pea seedlings. Plant growth analysis demonstrated that the "broken-stick" model fitted well with the growth pattern of all field pea genotypes and can be used to determine the linear growth phase. Further analysis suggested that the estimated plant parameters collected at the linear growth phase can effectively differentiate early vigour across field pea genotypes. High correlation between normalised difference vegetation indices captured from the field trial and estimated shoot biomass and top-view area confirmed the consistent performance of early vigour field pea genotypes under controlled and field environments. Overall, our results demonstrated that this robust screening tool is highly applicable and will enable breeding programs to rapidly identify early vigour traits and utilise germplasm to contribute to the genetic improvement of field peas

Effectiveness of three potential sources of resistance in wheat against Wheat streak mosaic virus under field conditions

Wheat streak mosaic virus is an established major threat to wheat in North America and is newly identified in Australia. Three genetic sources of resistance were examined, Wsm1 (from an alien translocation), Wsm2 (from CO960293-2), and c2652 (selected i

Validation of molecular markers associated with boron tolerance, powdery mildew resistance and salinity tolerance in field peas

Field pea (Pisum sativum L.) is an important grain legume consumed both as human food and animal feed. However, productivity in low rainfall regions can be significantly reduced by inferior soils containing high levels of boron and/or salinity. Furthermore, powdery mildew (Erysiphe pisi) disease also causes significant yield loss in warmer regions. Breeding for tolerance to these abiotic and biotic stresses are major aims for pea breeding programs and the application of molecular markers for these traits could greatly assist in developing improved germplasm at a faster rate. The current study reports the evaluation of a near diagnostic marker, PsMlo, associated with powdery mildew (PM) resistance and boron (B) tolerance as well as linked markers associated with salinity tolerance across a diverse set of pea germplasm. The PsMlo1 marker predicted the PM and B phenotypic responses with high levels of accuracy (>80%) across a wide range of field pea genotypes, hence offers the potential to be widely adapted in pea breeding programs. In contrast, linked markers for salinity tolerance were population specific, therefore, application of these markers would be suitable to relevant crosses within the program. Our results also suggest that there are possible new sources of salt tolerance present in field pea germplasm that could be further exploited

Identification and evaluation of resistance to powdery mildew and yellow rust in a wheat mapping population

<div><p>Deployment of cultivars with genetic resistance is an effective approach to control the diseases of powdery mildew (PM) and yellow rust (YR). Chinese wheat cultivar XK0106 exhibits high levels of resistance to both diseases, while cultivar E07901 has partial, adult plant resistance (APR). The aim of this study was to map resistance loci derived from the two cultivars and analyze their effects against PM and YR in a range of environments. A doubled haploid population (388 lines) was used to develop a framework map consisting of 117 SSR markers, while a much higher density map using the 90K Illumina iSelect SNP array was produced with a subset of 80 randomly selected lines. Seedling resistance was characterized against a range of PM and YR isolates, while field scores in multiple environments were used to characterize APR. Composite interval mapping (CIM) of seedling PM scores identified two QTLs (<i>QPm</i>.<i>haas-6A</i> and <i>QPm</i>.<i>haas-2A</i>), the former being located at the <i>Pm21</i> locus. These QTLs were also significant in field scores, as were <i>Qpm</i>.<i>haas-3A</i> and <i>QPm</i>.<i>haas-5A</i>. <i>QYr</i>.<i>haas-1B-1</i> and <i>QYr</i>.<i>haas-2A</i> were identified in field scores of YR and were located at the <i>Yr24/26</i> and <i>Yr17</i> chromosomal regions respectively. A second 1B QTL, <i>QYr</i>.<i>haas-1B-2</i> was also identified. <i>QPm</i>.<i>haas-2A</i> and <i>QYr</i>.<i>haas-1B-2</i> are likely to be new QTLs that have not been previously identified. Effects of the QTLs were further investigated in multiple environments through the testing of selected lines predicted to contain various QTL combinations. Significant additive interactions between the PM QTLs highlighted the ability to pyramid these loci to provide higher level of resistance. Interactions between the YR QTLs gave insights into the pathogen populations in the different locations as well as showing genetic interactions between these loci.</p></div

Mean severity of lines containing combinations of the indicated QTLs from the E07901 × XK0106 DH population, highlighting the additive effects of the QTLs to yellow rust in multiple locations in 2015.

<p>Mean severity of lines containing combinations of the indicated QTLs from the E07901 × XK0106 DH population, highlighting the additive effects of the QTLs to yellow rust in multiple locations in 2015.</p

Position and effects of quantitative trait loci (QTL) for seedling resistance to powdery mildew (PM) and adult plant resistance (APR) to PM and yellow rust (YR) in different environments (years).

<p>Position and effects of quantitative trait loci (QTL) for seedling resistance to powdery mildew (PM) and adult plant resistance (APR) to PM and yellow rust (YR) in different environments (years).</p

Linkage groups of wheat chromosomes showing SSR and SNP markers in QTL regions linked to resistance against powdery mildew (PM) and yellow rust (YR) in the DH population of E07901 × XK0106.

<p>Boxed QTLs show regions of significance at P≤0.05 and error bars at P≤0.1. Markers in bold highlight loci the peak marker for the associated QTL. Some related genes/QTLs were also shown in the LG by linked marker position in the consensus maps.</p

Genetic analysis of seedling resistance to <i>Bgt6-11</i> in a doubled haploid (DH) population derived from E07901 × XK0106.

<p>Genetic analysis of seedling resistance to <i>Bgt6-11</i> in a doubled haploid (DH) population derived from E07901 × XK0106.</p