Alfalfa ( Medicago sativa L.) is a globally vital forage crop valued for its perennial growth and multiple annual harvests. A breeding effort is underway to improve the crop for productivity and persistence against biotic and abiotic stresses using “creeping rootedness,” a trait where plants exhibit horizontal root growth, similar to rhizomes, with increased vegetative ground surface area. In this study, we genotyped a breeding population of 648 alfalfa lines segregating for creeping rootedness using the 3K DArTag marker panel to identify trait‐associated genomic loci and evaluate the feasibility of genomic prediction to accelerate breeding cycles. Using genome‐wide association studies (GWAS), we identified three quantitative trait loci (QTLs), with one major QTL located on chromosome 6.1 associated with this trait. Genomic prediction showed moderate predictive ability ( r = 0.68) for creeping rootedness. A significant advancement in this study was the development and utilization of the Breeding Insight Genomics Application (BIGapp), an R Shiny application designed to streamline the processing of genomic data through an intuitive interface. This tool makes integrating genomics into existing breeding programs accessible, regardless of species ploidy or the researcher's coding proficiency. The identified QTL will be essential in future efforts to develop new alfalfa cultivars with the creeping rootedness trait and accelerate the breeding cycle, with BIGapp playing a pivotal role in these advancements.

Muskellunge (Esox masquinongy) is the largest and most prized game fish in North America. However, little is known about Muskellunge genetic diversity in Iowa’s propagation program. We used Whole-Genome Sequencing of 12 brooding individuals from Iowa and publicly available RAD-seq of 625 individuals from the St. Lawrence River in Canada to study the genetic differences between populations, analyze signatures of selection, and evaluate the levels of genetic diversity in both populations. Given that there is no reference genome available, reads were aligned to the genome of Pike (Esox lucius). Variant calling produced 7,886,471 biallelic variants for the Iowa population and 16,867 high-quality SNPs that overlap with the Canadian samples. Principal component analysis (PCA) and Admixture analyses showed a large genetic difference between Canadian and Iowan populations. Window-based pooled heterozygosity found 6 highly heterozygous windows in the Iowa population and Fst between populations found 14 windows with fixation statistic (Fst) values larger than 0.9. Canadian inbreeding rate (Froh = 0.32) appears to be higher due to the inbreeding of Iowa population (Froh = 0.03), presumably due to isolation of subpopulations. Although inbreeding does not seem to be an immediate concern for Muskellunge in Iowa, the Canadian population seems to have a high rate of inbreeding. Finally, this approach can be used to assess the long-term viability of the current management practices of Muskellunge populations across North America.

Vitamin A is essential for human health, but current intake levels in many developing countries such as India are too low due to malnutrition. According to the World Health Organization, an estimated 250 million preschool children are vitamin A deficient globally. This number excludes pregnant women and nursing mothers, who are particularly vulnerable. Efforts to improve access to vitamin A are key because supplementation can reduce mortality rates in young children in developing countries by around 23%. Three key genes, BCMO1, BCO2, and SCARB1, have been shown to be associated with the amount of β-carotene (BC) in milk. Whole-genome sequencing reads from the coordinates of these 3 genes in 202 non-Indian cattle (141 Bos taurus, 61 Bos indicus) and 35 non-Indian buffalo (Bubalus bubalis) animals from several breeds were collected from data repositories. The number of SNP detected in the coding regions of these 3 genes ranged from 16 to 26 in the 3 species, with 5 overlapping SNP between B. taurus and B. indicus. All these SNP together with 2 SNP in the upstream part of the gene but already present in dbSNP (https://www.ncbi.nlm.nih.gov/projects/SNP/) were used to build a custom Sequenom array. Blood for DNA and milk samples for BC were obtained from 2,291 Indian cows of 5 different breeds (Gir, Holstein cross, Jersey Cross, Tharparkar, and Sahiwal) and 2,242 Indian buffaloes (Jafarabadi, Murrah, Pandharpuri, and Surti breeds). The DNA was extracted and genotyped with the Sequenom array. For each individual breed and the combined breeds, SNP with an association that had a P-value <0.3 in the first round of linear analysis were included in a second step of regression analyses to determine allele substitution effects to increase the content of BC in milk. Additionally, an F-test for all SNP within gene was performed with the objective of determining if overall the gene had a significant effect on the content of BC in milk. The analyses were repeated using a Bayesian approach to compare and validate the previous frequentist results. Multiple significant SNP were found using both methodologies with allele substitution effects ranging from 6.21 (3.13) to 9.10 (5.43) µg of BC per 100 mL of milk. Total gene effects exceeded the mean BC value for all breeds with both analysis approaches. The custom panel designed for genes related to BC production demonstrated applicability in genotyping of cattle and buffalo in India and may be used for cattle or buffalo from other developing countries. Moreover, the recommendation of selection for significant specific alleles of some gene markers provides a route to effectively increase the BC content in milk in the Indian cattle and buffalo populations.

Genomics-enabled selective animal breeding has become common in recent years, prompting a growing need for diverse genotyping tools that facilitate collaboration among research groups while meeting specific programme needs and objectives. Here, we report the development of a medium-density amplicon panel (DArTag) of 2,950 loci for North American Atlantic salmon. It includes loci distributed across the genome and loci useful for distinguishing the continent-of-origin, parentage, and sex determination. This mid-density panel offers more cost-effective and rapid genotyping capabilities for Atlantic salmon researchers and breeders. The open access provided by this platform facilitates comparisons and enhances data reusability across projects, institutions and countries that use different genomic tools for genotyping. This genotyping panel can make routine genotyping a viable tool for breeding and research programmes.