Faculty Opinions recommendation of Linkage mapping identifies the sex determining region as a single locus in the Pennate diatom Seminavis robusta.

The amplified fragment length polymorphism (AFLP) is a powerful marker, allowing rapid and simultaneous evaluation of multiple potentially polymorphic sites. Although well-adapted to linkage mapping and diversity assessment, AFLPs are primarily dominant in nature. Dominance, relatively high cost, and technological difficulty limit use of AFLPs for marker-aided selection and other locus-specific applications. In carrot the Y2 locus conditions carotene accumulation in the root xylem. We identified AFLP fragments linked to the dominant Y2 allele and pursued conversion of those fragments to codominant, PCR-based forms useful for locus-specific applications. The short length of AFLPs (≈60 to 500 bp) precludes development of longer, more specific primers as in SCAR development. Instead, using sequence information from cloned AFLP fragments for primer design, regions outside of the original fragment were amplified by inverse PCR or ligation-mediated PCR, cloned, and sequenced. Differences in sequences associated with Y2 vs. y2 allowed development of simple PCR assays differentiating those alleles. PCR primers flanking an insertion associated with the recessive allele amplified differently sized products for the two Y2 alleles in one assay. This assay is rapid, technologically simple (requiring no radioactivity and little advanced training or equipment), reliable, inexpensive, and codominant. Our PCR assay has a variety of large scale, locus-specific applications including genotyping diverse carrot cultivars and wild and feral populations. Efforts are underway to improve upon conversion technology and to more extensively test the techniques we have developed.

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Single-Locus and Multilocus Analysis of Genetic Differentiation of the Races of Man: A Critique

The American Naturalist ◽

10.1086/283356 ◽

1978 ◽

Vol 112 (988) ◽

pp. 1134-1138 ◽

Cited By ~ 4

Author(s):

Ranajit Chakraborty

Keyword(s):

Genetic Differentiation ◽

Single Locus ◽

Multilocus Analysis

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High-density linkage mapping for agronomic and physiological traits of rice (Oryza sativa L.) under reproductive-stage salt stress

Journal of Genetics ◽

10.1007/s12041-021-01301-6 ◽

2021 ◽

Vol 100 (2) ◽

Author(s):

Mostafa Ahmadizadeh ◽

Nadali Babaeian-Jelodar ◽

Ghasem Mohammadi-Nejad ◽

Nadali Bagheri ◽

Rakesh Kumar Singh

Keyword(s):

Oryza Sativa ◽

Salt Stress ◽

Linkage Mapping ◽

Oryza Sativa L ◽

High Density ◽

Reproductive Stage ◽

Physiological Traits

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Identification of Genomic Regions Associated with Concentrations of Milk Fat, Protein, Urea and Efficiency of Crude Protein Utilization in Grazing Dairy Cows

Genes ◽

10.3390/genes12030456 ◽

2021 ◽

Vol 12 (3) ◽

pp. 456

Author(s):

Hewa Bahithige Pavithra Chathurangi Ariyarathne ◽

Martin Correa-Luna ◽

Hugh Thomas Blair ◽

Dorian John Garrick ◽

Nicolas Lopez-Villalobos

Keyword(s):

Gene Ontology ◽

New Zealand ◽

Dairy Cows ◽

Candidate Genes ◽

Milk Fat ◽

Crude Protein ◽

Single Locus ◽

Protein Utilization ◽

Grazing Dairy Cows ◽

Genomic Regions

The objective of this study was to identify genomic regions associated with milk fat percentage (FP), crude protein percentage (CPP), urea concentration (MU) and efficiency of crude protein utilization (ECPU: ratio between crude protein yield in milk and dietary crude protein intake) using grazing, mixed-breed, dairy cows in New Zealand. Phenotypes from 634 Holstein Friesian, Jersey or crossbred cows were obtained from two herds at Massey University. A subset of 490 of these cows was genotyped using Bovine Illumina 50K SNP-chips. Two genome-wise association approaches were used, a single-locus model fitted to data from 490 cows and a single-step Bayes C model fitted to data from all 634 cows. The single-locus analysis was performed with the Efficient Mixed-Model Association eXpedited model as implemented in the SVS package. Single nucleotide polymorphisms (SNPs) with genome-wide association p-values ≤ 1.11 × 10−6 were considered as putative quantitative trait loci (QTL). The Bayes C analysis was performed with the JWAS package and 1-Mb genomic windows containing SNPs that explained > 0.37% of the genetic variance were considered as putative QTL. Candidate genes within 100 kb from the identified SNPs in single-locus GWAS or the 1-Mb windows were identified using gene ontology, as implemented in the Ensembl Genome Browser. The genes detected in association with FP (MGST1, DGAT1, CEBPD, SLC52A2, GPAT4, and ACOX3) and CPP (DGAT1, CSN1S1, GOSR2, HERC6, and IGF1R) were identified as candidates. Gene ontology revealed six novel candidate genes (GMDS, E2F7, SIAH1, SLC24A4, LGMN, and ASS1) significantly associated with MU whose functions were in protein catabolism, urea cycle, ion transportation and N excretion. One novel candidate gene was identified in association with ECPU (MAP3K1) that is involved in post-transcriptional modification of proteins. The findings should be validated using a larger population of New Zealand grazing dairy cows.

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