Biology subjects

Jordan, K. W.

Publications and source records attributed to Jordan, K. W..

4 recordsLinked to original sources

bioRxiv2025

Identification of stripe rust adult plant resistance genes in the hard winter wheat cultivar Bakers Ann

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is among the most destructive wheat diseases. Identifying resistance genes is crucial for the development of resistant cultivars. "Bakers Ann", a hard winter wheat cultivar developed by Oklahoma State University, has shown durable adult plant resistance to stripe rust. To dissect the genetic basis underlying stripe rust resistance in Bakers Ann, 125 doubled haploid lines, derived from the cross OK12D22004-016 x Bakers Ann, were evaluated at the adult plant stage in the greenhouse and in field environments in Oklahoma, Kansas, and Washington. This population was genotyped using genotyping-by-sequencing, which produced 7,268 single-nucleotide polymorphisms for genetic mapping. Quantitative trait loci (QTL) analysis identified six loci, four from Bakers Ann on chromosomes 2DL, 4BS, 4BL, and 7BL, and two from OK12D22004-016 on chromosomes 2AS and 2AL. Although OK12D22004-016 is susceptible in the US Great Plains, it was found to carry QYr.osu-2AS, which was linked to Yr17 on the 2NvS translocation and explained up to 30% of the phenotypic variation, but was effective in a single location in Washington. Two major QTL were identified in Bakers Ann, QYr.osu-2DL on chromosome 2DL that explained up to 57% of the phenotypic variation and mapped close to Yr54, and QYr.osu-4BL on chromosome 4BL that explained up to 15% of the phenotypic variation and mapped close to Yr62. Resistance in Bakers Ann resulted from additive effects of the four QTL. Two kompetitive allele-specific PCR markers were developed for QYr.osu-2DL to facilitate marker-assisted selection for stripe rust resistance.

genetics↗

bioRxiv2023

Natural genomic variation in rice blast genomes is associated with specific heterochromatinmodifications

Genome organization in eukaryotes exhibits non-random patterns tied to transcription, replication, and chromatin. However, the driving forces across these processes, and their impacts on genome evolution remain unclear. To address this, we analyzed sequence data from 86 Magnaporthe oryzae isolates, a globally important plant pathogenic fungus, alongside new reference genomes, to investigate DNA sequence variation and the epigenome. Histone modification profiles were obtained through genome-wide chromatin immunoprecipitation-sequencing of the four new reference strains, which revealed that repressive histone marks (H3K27me3, H3K9me3) were associated with SNP and INDEL frequency. Densely grouped SNPs were found to reside in heterochromatin, often outside transposable elements, highlighting the link between heterochromatin and DNA variation. Even when controlling for selection, silent SNP frequency/kb was higher in H3K27me3-associated genes. Effector genes, key to pathogenicity, also displayed this trend. Comparing the reference strains, euchromatic regions were often syntenic, while heterochromatic regions trended towards non-syntenic. Heterochromatin emerged as a major factor associated with diverse DNA variations in M. oryzae populations, even when accounting for selective pressure. This underscores heterochromatins pivotal role in shaping genetic diversity in these mainly asexually reproducing fungi.

evolutionary biology↗

bioRxiv2023

Allelic variation in the wheat homolog of topoisomerase II is associated with crossover rate

Meiotic recombination is a fundamental biological process that impacts genetic diversity and response of variants to selection. The increase in crossover (CO) frequency by modulating the activity of meiotic genes has been suggested as potential means to improve the efficiency of selection and mitigate the negative impact of linkage drag in crop improvement programs. In this study, we used the wheat nested association mapping (NAM) population to map QTL associated with CO rate and harboring TaTOPII-A1, a gene encoding topoisomerase II that is involved in the regulation of meiosis. An amino acid changing SNP (T/C) located in exon 19 of TaTOPII-A1 with a predicted functional effect showed an association with CO rate. The T-allele of TaTOPII-A1 was associated with a statistically significant 5.9 % increase in COs across several NAM families. The involvement of TaTOPII-A1 in processes affecting CO rate in wheat was confirmed using a TaTOPII-A1 mutant. A strong-effect missense mutation in the TaTOPII-A1 coding region resulted in 1.4-fold increase in the genetic map length and 53% increase in CO rate compared to the wild-type allele. These results demonstrate that functional mutations in TaTOPII-A1 can lead to increased CO frequency. The mutant and natural alleles of TaTOPII-A1 identified in our study could serve as new sources of recombination-promoting genes to manipulate CO rate in wheat and possibly other crops.

genetics↗

bioRxiv2021

The haplotype-based analysis of Aegilops tauschii introgression into hard red winter wheat and its impact on productivity traits

Introgression from wild relatives have a great potential to broaden beneficial allelic diversity available for crop improvement in breeding programs. Here, we assessed the impact of introgression from 21 diverse accessions of Aegilops tauschii, the diploid ancestor of the wheat D genome, into six hard red winter wheat cultivars on yield and yield component traits. We used 5.2 million imputed D genome SNPs identified by whole-genome sequencing of parental lines and the sequence-based genotyping of introgression population including 351 BC1F3:5 lines. Phenotyping data collected from the irrigated and non-irrigated field trials revealed that up to 23% of the introgression lines produce more grain than the parents and check cultivars. Based on sixteen yield stability statistics, the yield of twelve introgression lines (3.4%) was stable across treatments, years and locations; five of these lines were also high yielding, producing 9.8% more grain than the average yield of check cultivars. The most significant SNP-trait and haplotype-trait associations were identified on chromosome arms 2DS and 6DL for spikelet number per spike (SNS), on chromosome arms 2DS, 3DS, 5DS and 7DS for grain length and on chromosome arms 1DL, 2DS, 6DL and 7DS for grain width. Introgression of haplotypes from Ae. tauschii parents was associated with increase in SNS, which positively correlated with heading date, whereas haplotypes from hexaploid wheat parents were associated with increased grain width. We show that haplotypes on 2DS associated with increased spikelet number and heading date are linked with multiple introgressed alleles of Ppd-D1 identified by the whole-genome sequencing of the Ae. tauschii parents. While some introgressed haplotypes exhibited significant pleiotropic effects with the direction of effects on the yield component traits being largely consistent with the previously reported trade-offs, there were haplotype combinations associated with the positive trends in yield. The characterized repertoire of the introgressed haplotypes derived from Ae. tauschii accessions with the combined positive effects on yield and yield components traits in elite germplasm provides a valuable source of alleles for improving the productivity of winter wheat by optimizing the contribution of component traits to yield.

genetics↗