Characterization of wheat-Thinopyrum bessarabicum genetic stock for stripe rust and Karnal bunt resistance

Utilization of modern breeding techniques for developing high yielding and uniform plant types ultimately narrowing the genetic makeup of most crops. Narrowed genetic makeup of these crops has made them vulnerable towards disease and insect epidemics. For sustainable crop production, genetic variability of these crops must be broadened against various biotic and abiotic stresses. One of the ways to widen genetic configuration of these crops is to identify novel additional sources of durable resistance. In this regard crops wild relatives are providing valuable sources of allelic diversity towards various biotic, abiotic stress tolerance and quality components. For incorporating novel variability from wild relative’s wide hybridization technique has become a promising breeding method. For this purpose, wheat-Th. bessarabicum amphiploid, addition and translocation lines have been screened in field and screen house conditions to get novel sources of yellow rust and Karnal bunt resistant. Stripe rust screening under field conditions has revealed addition lines 4JJ and 6JJ as resistant to moderately resistant while addition lines 3JJ, 5JJ, 7JJ and translocation lines Tr-3, Tr-6 as moderately resistant wheat-Thinopyrum-bessarabicum genetic stock. Karnal bunt screening depicted addition lines 5JJ and 4JJ as highly resistant genetic stock. These genetic stocks may be used to introgression novel stripe rust and Karnal bunt resistance from the tertiary gene pool into susceptible wheat backgrounds.

Identification of Monoallelically Expressed Genes Associated with Economic Traits in Hanwoo (Korean Native Cattle)

Hanwoo, an indigenous Korean cattle breed, has been genetically improved by selecting superior sires called Korean-proven bulls. However, cows still contribute half of the genetic stock of their offspring, and allelic-specific expressed genes have potential, as selective targets of cows, to enhance genetic gain. The aim of this study is to identify genes that have MAEs based on both the genome and transcriptome and to estimate their effects on breeding values (BVs) for economically important traits in Hanwoo. We generated resequencing data for the parents and RNA-sequencing data for the muscle, fat, and brain tissues of the offspring. A total of 3801 heterozygous single nucleotide polymorphisms (SNPs) in offspring were identified and they were located in 1569 genes. Only 14 genes showed MAE (seven expressing maternal alleles and seven expressing paternal alleles). Tissue-specific MAE was observed, and LANCL1 showed maternal allele expression across all tissues. MAE genes were enriched for the biological process of cell death and angiogenesis, which included ACKR3 and PDCL3 genes, whose SNPs were significantly associated with BVs of lean meat production-related traits, such as weight at 12 months of age, carcass weight, and loin eye area. In the current study, monoallelically expressed genes were identified in various adult tissues and these genes were associated with genetic capacity in Hanwoo.

Kalanchoe ×forbesiae (Crassulaceae subfam. Kalanchooideae) derived from K. lubangensis × K. sexangularis: towards improved horticultural material

Efforts to broaden and improve the genetic stock from which horticultural material of Kalanchoe (Crassulaceae subfam. Kalanchooideae) is made available globally are on-going. Apart from making small, light-weight, highly floriferous material—both single- and double-flowered—available to the in- and outdoor plant trades, work is also underway to select Kalanchoe material that can be sold as long-lasting cut flowers. Material derived from K. lubangensis × K. sexangularis, here described as K. ×forbesiae, shows promise as a source of cut flowers.

Genomic variation in captive deer mouse (Peromyscus maniculatus) populations

Background Deer mice (genus Peromyscus) are the most common rodents in North America. Despite the availability of reference genomes for some species, a comprehensive database of polymorphisms, especially in those maintained as living stocks and distributed to academic investigators, is missing. In the present study we surveyed two populations of P. maniculatus that are maintained at the Peromyscus Genetic Stock Center (PGSC) for polymorphisms across their 2.5 × 109 bp genome. Results High density of variation was identified, corresponding to one SNP every 55 bp for the high altitude stock (SM2) or 207 bp for the low altitude stock (BW) using snpEff (v4.3). Indels were detected every 1157 bp for BW or 311 bp for SM2. The average Watterson estimator for the BW and SM2 populations is 248813.70388 and 869071.7671 respectively. Some differences in the distribution of missense, nonsense and silent mutations were identified between the stocks, as well as polymorphisms in genes associated with inflammation (NFATC2), hypoxia (HIF1a) and cholesterol metabolism (INSIG1) and may possess value in modeling pathology. Conclusions This genomic resource, in combination with the availability of P. maniculatus from the PGSC, is expected to promote genetic and genomic studies with this animal model.

Genetic melting pot and importance of long-distance dispersal indicated in the Gladiolus imbricatus L. populations in the Polish Carpathians

The genetic diversity in 11 populations of Gladiolus imbricatus in five mountain ranges, including the Tatra, Pieniny, Gorce, Beskid Niski (Western Carpathians) and Bieszczady Mts (Eastern Carpathians), was studied with inter-simple sequence repeat (ISSR) markers. The species is a perennial plant occurring in open and semi-open sites of anthropogenic origin (meadows and forest margins). We checked a hypothesis on the microrefugial character of the plant populations in the Pieniny Mts, a small calcareous Carpathian range of complicated relief that has never been glaciated. Plant populations in the Tatra and Pieniny Mts had the highest genetic diversity indices, pointing to their long-term persistence. The refugial vs. the non-refugial mountain ranges accounted for a relatively high value of total genetic variation [analysis of molecular variance (AMOVA), 14.12%, p = 0.003]. One of the Pieniny populations was of hybridogenous origin and shared genetic stock with the Tatra population, indicating there is a local genetic melting pot. A weak genetic structuring of populations among particular regions was found (AMOVA, 4.5%, p > 0.05). This could be an effect of the frequent short-distance and sporadic long-distance gene flow. The dispersal of diaspores between the remote populations in the Western Carpathians and Eastern Carpathians could be affected by the historical transportation of flocks of sheep from the Tatra to Bieszczady Mts.

A roadmap to Durable BCTV Resistance Using Long-Read Genome Assembly of Genetic Stock KDH13

Beet Curly Top (BCT) is a viral disease which negatively impacts crop productivity for sugar beet growers and the sugar beet industry in the western USA and dry regions worldwide. Current varieties exhibit little genetic resistance to the Beet Curly Top Virus (BCTV), suggesting there is a large potential for improvement. KDH13 (PI 663862) is a double-haploid line created from a population (C762-17/PI 560130) which segregates for resistance to BCTV and was identified as genetic stock for the improvement of sugar beet varieties. PacBio sequences were generated and assembled to better define the content and organization of variation within the KDH13 genome and to provide resources to identify specific variation underpinning durable genetic resistance. Using ab initio predicted proteins as anchors, the assembled KDH13 contigs were placed in a more contiguous order using the EL10.1 reference genome, which leveraged Bio-Nano optical maps and Hi-C proximity information for chromosome level scaffolding. In total, 4681 (75%) of the 6245 contigs were placed in the order and orientation of the EL10.1 genome. The anchored contigs represented 502,929,268 bp (87.7%), the KDH13 genome assembly. An F1 hybrid and parental lines KDH13 (resistant) and KDH19-17 (susceptible) were sequenced using Illumina technology in order to characterize the SNP, indel, and structural variation between parental lines and allow for a more detailed investigation into causal variation linked to important phenotypes. In total, 3,086,720 variants were detected, including 2,259,324 single-nucleotide polymorphisms, 191,448 insertions, 198,057 deletions, 268,090 complex substitutions, 90,004 multi allelic variants, and 79,797 structural variants. Of the total variation, 1,158,491 were informative in the F1 and were able to discriminate between the two parents. This information represents a high-density marker dataset distributed globally across the sugar beet genome and can be used to track genomic segments in populations where KDH13 is used as parental material to improve BCTV resistance.