G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data

SeqSNP-Based Targeted GBS Provides Insight into the Genetic Relationships among Global Collections of Brassica rapa ssp. oleifera (Turnip Rape)

Turnip rape is a multi-purpose crop cultivated in temperate regions. Due to its ability to fit into crop rotation systems and its role as a food and feed source, spring-type turnip rape cultivation is on the rise. To improve the crop's productivity and nutritional value, it is essential to understand its genetic diversity. In this study, 188 spring-type accessions were genotyped using SeqSNP, a targeted genotyping-by-sequencing method to determine genetic relationships between various groups and assess the potential effects of mutations within genes regulating major desirable traits. Single nucleotide polymorphism (SNP) alleles at six loci were predicted to have high effects on their corresponding genes' functions, whereas nine loci had country/region-specific alleles. A neighbor-joining cluster analysis revealed three major clusters (I to III). About 72% of cluster-I accessions were of Asian origin, whereas 88.5% of European accessions and all North American accessions were placed in cluster-II or cluster-III. A principal coordinate analysis explained 65.3% of the total genetic variation. An analysis of molecular variance revealed significant differentiation among different groups of accessions. Compared to Asian cultivars, European and North American cultivars share more genetic similarities. Hence, crossbreeding Asian and European cultivars may result in improved cultivars due to desirable allele recombination. Compared to landraces and wild populations, the cultivars had more genetic variation, indicating that breeding had not caused genetic erosion. There were no significant differences between Swedish turnip rape cultivars and the NordGen collection. Hence, crossbreeding with genetically distinct cultivars could enhance the gene pool's genetic diversity and facilitate superior cultivar development.

Whole-genome resequencing-based characterization of a durum wheat landrace showing similarity to 'Senatore Cappelli'

Durum wheat (Triticum turgidum spp. durum) is a major cereal adopted since antiquity to feed humans. Due to its use, dating back several millennia, this species features a wide genetic diversity and landraces are considered important repositories of gene pools which constitute invaluable tools for breeders. The aim of this work is to provide a first characterization of a wheat landrace, referred to as 'TB2018', that was collected in the Apulia region (Southern Italy). 'TB2018' revealed, through visual inspection, characters reminiscent of the traditional variety 'Senatore Cappelli', while exhibiting a distinctive trait, i.e., reduced stature. Indeed, the comparison with a set of Italian durum wheat cultivars conducted in this study, in which 24 CPVO plant descriptors were adopted, placed the 'TB2018' landrace in proximity to the 'Senatore Cappelli' cultivar. In addition, the close similarity between the two genotypes was confirmed by the analysis of the seed protein pattern. A relative reduction was detected for 'TB2018' root elongation in the early stages of plant growth. The 'TB2018' genome sequence, obtained through low-coverage resequencing and comparison to the reference 'Svevo' cultivar is also reported in this study, followed by a genome-wide comparison against 259 durum wheat accessions that placed 'TB2018' close to the 'Cappelli' reference. Hundreds of genes putatively affected by variants that possess Gene Ontology descriptors were detected, among which some were shown to be putatively linked to the morphological traits that distinguish 'TB2018' from 'Senatore Cappelli', Overall, this study poses the basis for a possible exploitation of 'TB2018' per se in cultivation or as a source of alternative alleles in the breeding of traditional cultivars. This work also presents a genomic methodology that exploits the information contained in a low-depth, whole-genome sequence to derive genotypic data useful for cross-platform (chip data) comparisons.

Finding needles in a haystack: identification of inter-specific introgressions in wheat genebank collections using low-coverage sequencing data

Recently, entire genebank collections of wheat have been extensively characterized with sequencing data. We have identified introgressions using these genotyping-by-sequencing and whole-genome sequencing data. On the basis of our results, we provide information about predicted introgressions at 1-Mb resolution for 9,172 wheat samples as a resource for breeders and scientists. We recommend that all plant genetic resources, including genebank collections, be characterized using a combination of variant calling and introgression prediction. This is necessary to identify potential duplicates in collections efficiently and reliably, and to select promising germplasms with potentially beneficial introgressions for further characterization and prospective breeding application.

Identification of Novel Broad-Spectrum Leaf Rust Resistance Sources from Khapli Wheat Landraces

Wheat leaf rust caused by Puccinia triticina Eriks is an important disease that causes yield losses of up to 40% in susceptible varieties. Tetraploid emmer wheat (T. turgidum ssp. Dicoccum), commonly called Khapli wheat in India, is known to have evolved from wild emmer (Triticum turgidum var. dicoccoides), and harbors a good number of leaf rust resistance genes. In the present study, we are reporting on the screening of one hundred and twenty-three dicoccum wheat germplasm accessions against the leaf rust pathotype 77-5. Among these, an average of 45.50% of the germplasms were resistant, 46.74% were susceptible, and 8.53% had mesothetic reactions. Further, selected germplasm lines with accession numbers IC138898, IC47022, IC535116, IC535133, IC535139, IC551396, and IC534144 showed high level of resistance against the eighteen prevalent pathotypes. The infection type varied from ";", ";N", ";N1" to ";NC". PCR-based analysis of the resistant dicoccum lines with SSR marker gwm508 linked to the Lr53 gene, a leaf rust resistance gene effective against all the prevalent pathotypes of leaf rust in India and identified from a T. turgidum var. dicoccoides germplasm, indicated that Lr53 is not present in the selected accessions. Moreover, we have also generated 35K SNP genotyping data of seven lines and the susceptible control, Mandsaur Local, to study their relationships. The GDIRT tool based on homozygous genotypic differences revealed that the seven genotypes are unique to each other and may carry different resistance genes for leaf rust.