Quantitative Trait Loci for Resistance to Potato Dry Rot Caused by Fusarium sambucinum

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11-36 and 12-3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars.

Assessment of the Genetic Diversity of Chrysanthemum Cultivars Using SSR Markers

Chrysanthemums are undoubtedly one of the most popular flowering plants in the world. Their exceptional importance in Asian culture resulted in the global popularization of this species, which resulted in the high interest of breeders. Chrysanthemums can be divided into three groups: small-flowered, mid-flowered, and large-flowered. The exceptional economic importance and a large number of varieties make them problematic to identify, resulting in a less efficient breeding process. In the case of chrysanthemums, genotypes are almost impossible to distinguish by using phenotypic methods due to the high variation in morphological characteristics, even when they belong to the same group. The aim of the study was to evaluate the genetic diversity of 97 chrysanthemum cultivars using 14 selected SSR markers. Large-flowered varieties (Angali and Rosee D’une) were characterized by the smallest mutual distance, and the greatest distance was between large-flowered (Impact Rood) and small-flowered (Conaco Yellow) varieties. All methods of visualizing the results reveal a clear distinctiveness of small-flowered cultivars, except for the cultivars from the Moira series.

Efficient breeding of industrial brewing yeast strains using CRISPR/Cas9-aided mating-type switching

Yeast breeding is a powerful tool for developing and improving brewing yeast in a number of industry-relevant respects. However, breeding of industrial brewing yeast can be challenging, as strains are typically sterile and have large complex genomes. To facilitate breeding, we used the CRISPR/Cas9 system to generate double-stranded breaks in the MAT locus, generating transformants with a single specified mating type. The single mating type remained stable even after loss of the Cas9 plasmid, despite the strains being homothallic, and these strains could be readily mated with other brewing yeast transformants of opposite mating type. As a proof of concept, we applied this technology to generate yeast hybrids with an aim to increase β-lyase activity for fermentation of beer with enhanced hop flavour. First, a genetic and phenotypic pre-screening of 38 strains was carried out in order to identify potential parent strains with high β-lyase activity. Mating-competent transformants of eight parent strains were generated, and these were used to generate over 60 hybrids that were screened for β-lyase activity. Selected phenolic off-flavour positive (POF +) hybrids were further sporulated to generate meiotic segregants with high β-lyase activity, efficient wort fermentation, and lack of POF, all traits that are desirable in strains for the fermentation of modern hop-forward beers. Our study demonstrates the power of combining the CRISPR/Cas9 system with classic yeast breeding to facilitate development and diversification of brewing yeast. Key points • CRISPR/Cas9-based mating-type switching was applied to industrial yeast strains. • Transformed strains could be readily mated to form intraspecific hybrids. • Hybrids exhibited heterosis for a number of brewing-relevant traits.

Integrative Pre-Breeding for Biotic Resistance in Forest Trees

Climate change is unleashing novel biotic antagonistic interactions for forest trees that may jeopardize populations’ persistence. Therefore, this review article envisions highlighting major opportunities from ecological evolutionary genomics to assist the identification, conservation, and breeding of biotic resistance in forest tree species. Specifically, we first discuss how assessing the genomic architecture of biotic stress resistance enables us to recognize a more polygenic nature for a trait typically regarded Mendelian, an expectation from the Fisherian runaway pathogen–host concerted arms-race evolutionary model. Secondly, we outline innovative pipelines to capture and harness natural tree pre-adaptations to biotic stresses by merging tools from the ecology, phylo-geography, and omnigenetics fields within a predictive breeding platform. Promoting integrative ecological genomic studies promises a better understanding of antagonistic co-evolutionary interactions, as well as more efficient breeding utilization of resistant phenotypes.

RGB images-based vegetative index for phenotyping kenaf (Hibiscus cannabinus L.)

Kenaf (Hibiscus cannabinus L.) is an industrial crop used as a raw material in various fields and is cultivated worldwide. Compared to high potential for its utilization, breeding sector is not vigorous partially due to laborous breeding procedure. Thus, efficient breeding methods are required for varieties that can adapt to various environments and obtain optimal production. For that, identifying kenaf’s characteristics is very important during the breeding process. Here, we investigated if RGB based vegetative index (VI) could be associated with traits for biomass. We used 20 varieties and germplasm of kenaf and RGB images taken with unmanned aerial vehicles (UAVs) for field selection in early and late growth stage. In addition, measuring the stem diameter and the number of nodes confirmed whether the vegetative index value obtained from the RGB image could infer the actual plant biomass. Based on the results, it was confirmed that the individual surface area and estimated plant height, which were identified from the RGB image, had positive correlations with the stem diameter and node number, which are actual growth indicators of the rate of growth further, biomass could also be estimated based on this. Moreover, it is suggested that VIs have a high correlation with actual growth indicators; thus, the biomass of kenaf could be predicted. Interstingly, those traits showing high correlation in the late stage had very low correlations in the early stage. To sum up, the results in the current study suggest a more efficient breeding method by reducing labor and resources required for breeding selection by the use of RGB image analysis obtained by UAV. This means that considerable high-quality research could be performed even with a tight budget. Furthermore, this method could be applied to crop management, which is done with other vegetative indices using a multispectral camera.

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by FST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

Mapping Recombination Landscape and Basidial Spore Number in the Button Mushroom Agaricus bisporus

The button mushroom Agaricus bisporus is represented mainly by two varieties, a secondarily homothallic variety with predominantly two heterokaryotic spores per basidia and a heterothallic variety with predominantly four homokaryotic spored basidium. Both varieties also differ in their recombination landscape with the former showing crossovers (CO) predominantly at chromosome ends whereas the latter has a more evenly distribution of CO over the chromosomes. The two varieties are compatible, and this has been used to study segregation of the basidial spore number (BSN) and the genomic positions of recombination, i.e., the CO landscape, in order to find the underlying genetic determinants. Knowledge on genes controlling CO positions might facilitate either the conservation of favorable allele combinations or the disruption of unwanted allele combinations to reduce linkage drag. For BSN, in total seven QTL were found with the major QTL on chromosome 1 explaining ca. 55% of the phenotypic variation. It appeared, however, difficult to map the recombination landscape. This phenotype can only be assessed in the meiotic offspring of an intervarietal hybrid which is a laborious and difficult task. Nevertheless, this was done, and we were able to map three QTLs for this trait, two on chromosome 1 and one on chromosome 2 not overlapping with the QTL for BSN. The hurdles encountered are discussed and a new strategy is proposed that can solves these. We propose to use two genetically unrelated mapping populations both offspring of a cross between a var. bisporus and a var. burnettii homokaryon and thus segregating both for CO and BSN. Homokaryotic offspring of both populations can be intercrossed without limitation of mating incompatibility and marker homozygosity and the hybrid mushrooms directly used to map BSN. Homokaryotic offspring of these hybrid mushrooms can be genotypes to assess CO positions using next generation sequencing technologies that will solve marker problems encountered, especially for genotyping chromosome ends. This new approach can be a useful strategy for a more efficient breeding strategy for mushrooms in general.

Dynamic Diversity of NLR Genes in Triticum and Mining of Promising NLR Alleles for Disease Resistance

Bread wheat is an essential crop with the second-highest global production after maize. Currently, wheat diseases are a serious threat to wheat production. Therefore, efficient breeding for disease resistance is extremely urgent in modern wheat. Here, we identified 2012 NLR genes from hexaploid wheat, and Ks values of paired syntenic NLRs showed a significant peak at 3.1–6.3 MYA, which exactly coincided with the first hybridization event between A and B genome lineages at ~5.5 MYA. We provided a landscape of dynamic diversity of NLRs from Triticum and Aegilops and found that NLR genes have higher diversity in wild progenitors and relatives. Further, most NLRs had opposite diversity patterns between genic and 2 Kb-promoter regions, which might respectively link sub/neofunctionalization and loss of duplicated NLR genes. Additionally, we identified an alien introgression of chromosome 4A in tetraploid emmer wheat, which was similar to that in hexaploid wheat. Transcriptome data from four experiments of wheat disease resistance helped to profile the expression pattern of NLR genes and identified promising NLRs involved in broad-spectrum disease resistance. Our study provided insights into the diversity evolution of NLR genes and identified beneficial NLRs to deploy into modern wheat in future wheat disease-resistance breeding.

Polymorphisms of Codons 110, 146, 211 and 222 at the Goat PRNP Locus and Their Association with Scrapie in Greece

Scrapie is considered an endemic disease in both sheep and goats in Greece. However, contrary to sheep, in goats more than one prion protein (PrP) polymorphism has been recognized as a candidate for resistance breeding against the disease. For an impression, candidates which are circulating, (i) brain samples (n = 525) from scrapie-affected (n = 282) and non-affected (n = 243) animals within the national surveillance program, and (ii) individual blood samples (n = 1708) from affected (n = 241) and non-affected (n = 1467) herds, in a large part of mainland Greece and its islands, were collected and assayed. A dedicated Taqman method was used to test for amino acid polymorphisms 110T/P, 146N/S/D, 211R/Q, and 222Q/K. Highly prevalent genotypes were 110TT, 146NN, 211RR, and 222QQ. The frequencies of polymorphisms in blood and negative brain samples for codons 110P, 211Q, and 222K were 4.0%, 3.0%, and 1.9%, respectively, while 146D (0.7%) was present only on Karpathos island. Codon 110P was exclusively found in scrapie-negative brains, and homozygous 110P/P in two scrapie-negative goats. It is concluded that breeding programs in Karpathos could focus on codon 146D, while in other regions carriers of the 110P and 222K allele should be sought. Case-control and challenge studies are now necessary to elucidate the most efficient breeding strategies.