Biology subjects

Tello-Ruiz, M. K.

Publications and source records attributed to Tello-Ruiz, M. K..

4 recordsLinked to original sources

bioRxiv2026

Development and evaluation of a cost-effective, mid-density SNP array as a sorghum community genotyping resource

The development of accessible and cost-effective genotyping platforms is essential to accelerate genetic gain in crop improvement. To address the U.S. sorghum communitys need for a standardized, mid-density genotyping resource, we developed and validated a targeted single-nucleotide polymorphism (SNP) array using the PlexSeq next-generation sequencing (NGS) platform. The resulting genotyping array includes 2,421 SNPs spanning all ten Sorghum bicolor chromosomes and integrates trait-linked and quality control markers selected by public and private stakeholders. Genotyping 2,726 diverse accessions, including the Sorghum Association Panel (SAP), demonstrated high call rates (>90% for most samples and markers), low missing data, and accurate resolution of population structure consistent with prior whole-genome studies. In comparative genomic prediction analyses, the mid-density array performed equivalently to high-density genotype-by-sequencing (GBS) platforms for key traits such as grain yield and plant height across multi-environment trials. Designed for broad utility in breeding pipelines, the array enables marker-assisted selection, genomic prediction, identity verification, and germplasm quality control. Moreover, its adoption by the USDA National Plant Germplasm System facilitates the curation of genebanks and the management of core collections. This community-driven genotyping platform offers a scalable, reproducible, and customizable tool to support molecular breeding in sorghum and underscores the value of targeted marker systems in resource-optimized crop improvement programs.

plant biology↗

bioRxiv2022

An improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype

The genome sequence assembly of the diploid and highly homozygous V. vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements of the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, despite the PN40024 genome is nearly homozygous, it still contains various heterozygous regions. Taking the opportunity of the improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences and considering that several Vitis sp. genomes have recently been assembled with these approaches, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased. The number of scaffolds decreased from 2,059 to 640 and the number of N bases was reduced by 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the amount of unplaced scaffolds were reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation to date of 35,230 genes. Finally, we demonstrate that PN40024 resulted from selfings of cv. Helfensteiner (cross of cv. Pinot noir and Schiava grossa) instead of a single Pinot noir. These advances will help maintaining the PN40024 genome as a gold-standard reference also contributing in the eventual elaboration of the grapevine pangenome.

genomics↗

bioRxiv2021

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The data indicate that the number of pan-genes exceeds 103,000 and that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres further reveal the locations and internal structures of major cytological landmarks. We show that combining structural variation with SNPs can improve the power of quantitative mapping studies. Finally, we document variation at the level of DNA methylation, and demonstrate that unmethylated regions are enriched for cis-regulatory elements that overlap QTL and contribute to changes in gene expression. One sentence summaryA multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

genomics↗

bioRxiv2019

Double triage to identify poorly annotated genes in Maize: The missing link in community curation

The sophistication of gene prediction algorithms and the abundance of RNA-based evidence for the maize genome may suggest that manual curation of gene models is no longer necessary. However, quality metrics generated by the MAKER-P gene annotation pipeline identified 17,225 of 130,330 (13%) protein-coding transcripts in the B73 Reference Genome V4 gene set with models of low concordance to available biological evidence. Working with eight graduate students, we used the Apollo annotation editor to curate 86 transcript models flagged by quality metrics and a complimentary method using the Gramene gene tree visualizer. All of the triaged models had significant errors - including missing or extra exons, non-canonical splice sites, and incorrect UTRs. A correct transcript model existed for about 60% of genes (or transcripts) flagged by quality metrics; we attribute this to the convention of elevating the transcript with the longest coding sequence (CDS) to the canonical, or first, position. The remaining 40% of flagged genes resulted in novel annotations and represent a manual curation space of about 10% of the maize genome (~4,000 protein-coding genes). MAKER-P metrics have a specificity of 100%, and a sensitivity of 85%; the gene tree visualizer has a specificity of 100%. Together with the Apollo graphical editor, our double triage provides an infrastructure to support the community curation of eukaryotic genomes by scientists, students, and potentially even citizen scientists.

bioinformatics↗