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Net form net blotch (NFNB), caused by the fungal pathogen Pyrenophora teres f. teres, is an important foliar disease present in all barley-producing regions of the world. This fungus is a hemibiotrophic and heterothallic ascomycete, where sexual recombination can lead to changes in disease expression in the host. Knowledge of the genetic architecture and genes involved in virulence is vital to increase the durability of NFNB resistance in barley cultivars. We used a genome-wide association mapping approach to characterize P. teres f. teres genomic regions associated with virulence in Australian barley cultivars. One hundred eighty-eight P. teres f. teres isolates collected across five Australian states were genotyped using Diversity Arrays Technology sequence markers and phenotyped across 20 different barley genotypes. Association mapping identified 14 different genomic regions associated with virulence, with the majority located on P. teres f. teres chromosomes 3 and 5 and one each present on chromosomes 1, 6, and 9. Four of the regions identified were confirmed by quantitative trait loci (QTL) mapping. The QTL regions are discussed in the context of their genomic architecture together with examination of their gene contents, which identified 20 predicted effectors. The number of QTL shown in this study at the population level clearly illustrates a complex genetic basis of P. teres f. teres virulence compared with pure necrotrophs, such as the wheat pathogens Parastagonospora nodorum and Parastagonospora tritici-repentis.

Pea weevil (Bruchus pisorum) is a damaging insect pest affecting pea (Pisum sativum) production worldwide. No resistant cultivars are available, although some levels of incomplete resistance have been identified in Pisum germplasm. To decipher the genetic control underlying the resistance previously identify in P. sativum ssp. syriacum, a recombinant inbred line (RIL F8:9) population was developed. The RIL was genotyped through Diversity Arrays Technology PL’s DArTseq platform and screened under field conditions for weevil seed infestation and larval development along 5 environments. A newly integrated genetic linkage map was generated with a subset of 6,540 markers, assembled into seven linkage groups, equivalent to the number of haploid pea chromosomes. An accumulated distance of 2,503 cM was covered with an average density of 2.61 markers cM−1. The linkage map allowed the identification of three QTLs associated to reduced seed infestation along LGs I, II and IV. In addition, a QTL for reduced larval development was also identified in LGIV. Expression of these QTLs varied with the environment, being particularly interesting QTL BpSI.III that was detected in most of the environments studied. This high-saturated pea genetic map has also allowed the identification of seven potential candidate genes co-located with QTLs for marker-assisted selection, providing an opportunity for breeders to generate effective and sustainable strategies for weevil control.

[Background] Pea (Pisum sativum) is one of the most important temperate grain legumes in the world, and its production is severely constrained by the pea aphid (Acyrthosiphon pisum). Wild relatives, such as P. fulvum, are valuable sources of allelic diversity to improve the genetic resistance of cultivated pea species against A. pisum attack. To unravel the genetic control underlying resistance to the pea aphid attack, a quantitative trait loci (QTL) analysis was performed using the previously developed high density integrated genetic linkage map originated from an intraspecific recombinant inbred line (RIL) population (P. fulvum: IFPI3260 × IFPI3251)., [Results] We accurately evaluated specific resistance responses to pea aphid that allowed the identification, for the first time, of genomic regions that control plant damage and aphid reproduction. Eight QTLs associated with tolerance to pea aphid were identified in LGs I, II, III, IV and V, which individually explained from 17.0% to 51.2% of the phenotypic variation depending on the trait scored, and as a whole from 17.0% to 88.6%. The high density integrated genetic linkage map also allowed the identification of potential candidate genes co‐located with the QTLs identified., [Conclusions] Our work shows how the survival of P. fulvum after the pea aphid attack depends on the triggering of a multi‐component protection strategy that implies a quantitative tolerance. The genomic regions associated with the tolerance responses of P. fulvum during A. pisum infestation have provided six potential candidate genes that could be useful in marker‐assisted selection (MAS) and genomic assisted breeding (GAB) after functional validation in the future. © 2019 Society of Chemical Industry

Macadamia (Macadamia integrifolia Maiden & Betche, Macadamia tetraphylla L.A.S. Johnson and their hybrids) is grown commercially around the world for its high-quality edible kernel. Traditional breeding efforts involve crossing varieties to produce thousands of progeny seedlings for evaluation. Cultivar improvement for nut yield using component traits and genomics are options for macadamia breeding, but accurate knowledge of genetic diversity and structure of the breeding population is required. This study reports allelic diversity within and between families of 295 seedling offspring from 29 parents, population structure and the extent of linkage disequilibrium (LD) in the population. Genotyping generated 19,527 silicoDArT and 5329 SNP markers, and, after filtering, 16,171 silicoDArTs and 4113 SNPs were used for diversity analyses. LD decay was initially rapid at short distances, but low-level LD persisted for long distances, with an average r2 = 0.124 for SNPs within 1 kb of each other. The seedling population was relatively genetically diverse and very similar to that of the 29 parents. The diversity (HE = 0.255 for progeny and 0.250 for parents) among these individuals indicates the level of diversity at the wider population level in the breeding programme, though the population appears less diverse than other fruit crops. Macadamia progeny was moderately differentiated (FST = 0.401) and formed k = 3 distinct clusters, which represents M. integrifolia germplasm separating from two different hybrid groups. There was low to no relationship between heterozygosity and performance for nut yield among progeny. These findings will inform future genomic studies of the Australian macadamia breeding programme, such as genome-wide association studies and genomic selection, where knowledge and control of population structure are vital.

Bread wheat (Triticum aestivum L.) is a staple food for a significant part of the world's population. The growing demand on its production can be satisfied by improving yield and resistance to biotic and abiotic stress. Knowledge of the genome sequence would aid in discovering genes and QTLs underlying these traits and provide a basis for genomics-assisted breeding. Physical maps and BAC clones associated with them have been valuable resources from which to generate a reference genome of bread wheat and to assist map-based gene cloning. As a part of a joint effort coordinated by the International Wheat Genome Sequencing Consortium, we have constructed a BAC-based physical map of bread wheat chromosome arm 7DS consisting of 895 contigs and covering 94% of its estimated length. By anchoring BAC contigs to one radiation hybrid map and three high resolution genetic maps, we assigned 73% of the assembly to a distinct genomic position. This map integration, interconnecting a total of 1713 markers with ordered and sequenced BAC clones from a minimal tiling path, provides a tool to speed up gene cloning in wheat. The process of physical map assembly included the integration of the 7DS physical map with a whole-genome physical map of Aegilops tauschii and a 7DS Bionano genome map, which together enabled efficient scaffolding of physical-map contigs, even in the non-recombining region of the genetic centromere. Moreover, this approach facilitated a comparison of bread wheat and its ancestor at BAC-contig level and revealed a reconstructed region in the 7DS pericentromere.

Motivation: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. Results: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases.

The high carotenoid content and distinctive carotenoid profile of tritordeum are conferred by its wild progenitor, Hordeum chilense. Genetic studies on this wild barley could exploit the knowledge gained in Hordeum vulgare L. if the synteny between H. vulgare and H. chilense is established. DArTSeq markers were aligned to barley genome and used to inspect H. chilense-barley synteny. All chromosome pairs showed a good degree of collinearity with the exception of 7Hv–7Hch, where a reciprocal translocation in 7Hch was identified. Carotenoid analyses revealed a high diversity for total carotenoids, free and esterified lutein in a collection of H. chilense. Population structure analyses revealed the existence of two subgroups contrasting for total carotenoids, free lutein and esterified lutein in seeds. Lutein esters were produced with palmitic and linoleic acids as happens in tritordeum. However, tritordeum prefer palmitic acid for the synthesis of lutein esters but this preference is not maintained in H. chilense. This indicates the existence of diversity in the enzymes involved in the esterification which could be useful in tritordeum breeding. Furthermore, several accessions produced lutein monoesters but they lacked diesters which suggests that esterification is controlled by more than one enzyme in H. chilense. A total of 91 marker-trait associations were identified for carotenoid content and profile. These associations constitute a good starting point for future genetic analyses for the identification of candidate genes from H. vulgare genome.

PR, IFPRI3; DCA, EPTD, Accurate crop varietal identification is the backbone of any high-quality assessment of outcomes and impacts. Sweetpotato (Ipomoea batatas) varieties have important nutritional differences, and there is a strong interest to identify nutritionally superior varieties for dissemination. In agricultural household surveys, such information is often collected based on the farmer's self-report. In this article, we present the results of a data capture experiment on sweet potato varietal identification in southern Ethiopia. Three household-based methods of identifying varietal adoption are tested against the benchmark of DNA fingerprinting: (A) Elicitation from farmers with basic questions for the most widely planted variety; (B) Farmer elicitation on five sweet potato phenotypic attributes by showing a visual-aid protocol; and (C) Enumerator recording observations on five sweet potato phenotypic attributes using a visual-aid protocol and visiting the field. In total, 20% of farmers identified a variety as improved when in fact it was local and 19% identified a variety as local when it was in fact improved. The variety names given by farmers delivered inconsistent and inaccurate varietal identities. Visual-aid protocols employed in methods B and C were better than those in method A, but greatly underestimated the adoption estimates given by the DNA fingerprinting method. Our results suggest that estimating the adoption of improved varieties with methods based on farmer self-reports is questionable and point towards a wider use of DNA fingerprinting in adoption and impact assessments.

Hexaploid tritordeum (×Tritordeum martinii A. Pujadas) (Pujadas 2016) has become a new crop due to its functional characteristics. The most important one is the golden colour of its flour which is caused by the presence of carotenoids (Atienza et al. 2007a). This amphiploid was obtained after chromosome doubling of the hybrid between Hordeum chilense and durum wheat (Martín & Sánchez-Monge 1982). H. chilense genes are responsible for the high carotenoid content (Atienza et al. 2007b; Rodríguez-Suárez et al. 2014) and the distinctive esterification profile of carotenoids (Mellado-Ortega and Hornero-Méndez 2015).

Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL) population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM−1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%). QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain) and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2) was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.