scholarly journals Correcting Pervasive Errors in Genotypic Datasets to Develop Genetic Maps

Agronomy ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 196
Author(s):  
Sadal Hwang ◽  
Tong Geon Lee
Keyword(s):  
Genetic Variation ◽  
Plant Species ◽  
Genetic Linkage Map ◽  
Gene Action ◽  
Genetic Maps ◽  
Potential Contribution ◽  
Phenotypic Data ◽  
Stepwise Procedure ◽  
Mapping Populations

Genetic mapping studies provide improved estimates for novel genomic loci, allelic effects and gene action controlling important traits. Such mapping studies are regularly performed by using a combination of genotypic data (e.g., genotyping markers tagging genetic variation within populations) and phenotypic data of appropriately structured mapping populations. Randomly obtained DNA information and more recent high-throughput genome sequencing efforts have dramatically increased the ability to obtain genetic markers for any plant species. Despite the presence of constantly and rapidly increasing genotypic data, necessary steps to determine whether specific markers can be associated with genetic variation may often be initially neglected, meaning that ever-growing genotypic markers do not necessarily maximize the power of mapping studies and often generate false results. To address this issue, we present a framework for analyzing genotypic data while developing a genetic linkage map. Our goal is to raise awareness of a stepwise procedure in the development of genetic maps as well as to outline the current and potential contribution of this procedure to minimize bias caused by errors in genotypic datasets. Empirical results obtained from the R/qtl package for the statistical language/software R are prepared with details of how we handled genotypic data to develop the genetic map of a major plant species. This study provides a stepwise procedure to correct pervasive errors in genotypic data while developing genetic maps. For use in custom follow-up studies, we provide input files and written R codes.

scholarly journals QTL Analysis of Five Morpho-Physiological Traits in Bread Wheat Using Two Mapping Populations Derived from Common Parents

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 604
Author(s):  
Paolo Vitale ◽  
Fabio Fania ◽  
Salvatore Esposito ◽  
Ivano Pecorella ◽  
Nicola Pecchioni ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Heading Date ◽  
Tiller Number ◽  
Genetic Maps ◽  
Yield Potential ◽  
Adaptation To Climate Change ◽  
Map Resolution ◽  
Mapping Populations

Traits such as plant height (PH), juvenile growth habit (GH), heading date (HD), and tiller number are important for both increasing yield potential and improving crop adaptation to climate change. In the present study, these traits were investigated by using the same bi-parental population at early (F2 and F2-derived F3 families) and late (F6 and F7, recombinant inbred lines, RILs) generations to detect quantitative trait loci (QTLs) and search for candidate genes. A total of 176 and 178 lines were genotyped by the wheat Illumina 25K Infinium SNP array. The two genetic maps spanned 2486.97 cM and 3732.84 cM in length, for the F2 and RILs, respectively. QTLs explaining the highest phenotypic variation were found on chromosomes 2B, 2D, 5A, and 7D for HD and GH, whereas those for PH were found on chromosomes 4B and 4D. Several QTL detected in the early generations (i.e., PH and tiller number) were not detected in the late generations as they were due to dominance effects. Some of the identified QTLs co-mapped to well-known adaptive genes (i.e., Ppd-1, Vrn-1, and Rht-1). Other putative candidate genes were identified for each trait, of which PINE1 and PIF4 may be considered new for GH and TTN in wheat. The use of a large F2 mapping population combined with NGS-based genotyping techniques could improve map resolution and allow closer QTL tagging.

scholarly journals An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 282-295 ◽  
Author(s):  
Elizabeth S Jones ◽  
Natalia L Mahoney ◽  
Michael D Hayward ◽  
Ian P Armstead ◽  
J Gilbert Jones ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Linkage Map ◽  
Genetic Map ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Genetic Linkage Map ◽  
Population Based ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

scholarly journals Recombinant inbred lines derived from cultivars of pea for understanding the genetic basis of variation in breeders' traits

2018 ◽  
Vol 16 (5) ◽  
pp. 424-436 ◽  
Author(s):  
Carol Moreau ◽  
Maggie Knox ◽  
Lynda Turner ◽  
Tracey Rayner ◽  
Jane Thomas ◽  
...  
Keyword(s):  
Recombinant Inbred ◽  
Seed Weight ◽  
Genetic Basis ◽  
Recombinant Inbred Lines ◽  
Field Trials ◽  
Genetic Maps ◽  
Genotypic Differences ◽  
Phenotypic Data ◽  
Growing Seasons ◽  
Randomized Field Trials

AbstractIn order to gain an understanding of the genetic basis of traits of interest to breeders, the pea varieties Brutus, Enigma and Kahuna were selected, based on measures of their phenotypic and genotypic differences, for the construction of recombinant inbred populations. Reciprocal crosses were carried out for each of the three pairs, and over 200 F2 seeds from each cross advanced to F13. Bulked F7 seeds were used to generate F8–F11 bulks, which were grown in triplicated plots within randomized field trials and used to collect phenotypic data, including seed weight and yield traits, over a number of growing seasons. Genetic maps were constructed from the F6 generation to support the analysis of qualitative and quantitative traits and have led to the identification of four major genetic loci involved in seed weight determination and at least one major locus responsible for variation in yield. Three of the seed weight loci, at least one of which has not been described previously, were associated with the marrowfat seed phenotype. For some of the loci identified, candidate genes have been identified. The F13 single seed descent lines are available as a germplasm resource for the legume and pulse crop communities.

scholarly journals Quantitative Trait Loci for Resistance to Potato Dry Rot Caused by Fusarium sambucinum

Agronomy ◽  
2022 ◽  
Vol 12 (1) ◽  
pp. 203
Author(s):  
Sylwester Sobkowiak ◽  
Marta Janiszewska ◽  
Emil Stefańczyk ◽  
Iwona Wasilewicz-Flis ◽  
Jadwiga Śliwka
Keyword(s):  
Interval Mapping ◽  
Potato Cultivars ◽  
Genetic Maps ◽  
Dry Rot ◽  
Potato Genome ◽  
Polygenic Control ◽  
Efficient Breeding ◽  
Chromosome I ◽  
Mapping Populations ◽  
Important Disease

Tuber dry rot is an important disease of potato caused by soil and seed-borne pathogens of the Fusarium genus leading to losses that may reach 60% of the yield. The goal of this work was to study the inheritance of the dry rot resistance in two diploid potato hybrid populations (11-36 and 12-3) with complex pedigrees, including several wild Solanum spp. We used an aggressive isolate of F. sambucinum for phenotyping both progenies, parents, and standard potato cultivars in laboratory tuber tests, in three subsequent years. The QTL for dry rot resistance were mapped by interval mapping on existing genetic maps of both mapping populations. The most important and reproducible QTL for this trait was mapped on chromosome I and additional year- and population-specific QTL were mapped on chromosomes II, VII, IX, XI, and XII, confirming polygenic control of this resistance. This is the first study mapping the loci affecting tuber dry rot resistance in potato genome that can contribute to better understanding of potato-F. sambucinum interaction and to more efficient breeding of resistant potato cultivars.

scholarly journals Conservation genetics of the threatened plant species Physaria filiformis (Missouri bladderpod) reveals strong genetic structure and a possible cryptic species

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0247586
Author(s):  
Christine E. Edwards ◽  
Brooke C. Tessier ◽  
Joel F. Swift ◽  
Burgund Bassüner ◽  
Alexander G. Linan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic Structure ◽  
Plant Species ◽  
Genetic Drift ◽  
Rare Species ◽  
Ex Situ ◽  
Ouachita Mountains ◽  
Genetic Diversity And Structure ◽  
Genetic Clusters

Understanding genetic diversity and structure in a rare species is critical for prioritizing both in situ and ex situ conservation efforts. One such rare species is Physaria filiformis (Brassicaceae), a threatened, winter annual plant species. The species has a naturally fragmented distribution, occupying three different soil types spread across four disjunct geographical locations in Missouri and Arkansas. The goals of this study were to understand: (1) whether factors associated with fragmentation and small population size (i.e., inbreeding, genetic drift or genetic bottlenecks) have reduced levels of genetic diversity, (2) how genetic variation is structured and which factors have influenced genetic structure, and (3) how much extant genetic variation of P. filiformis is currently publicly protected and the implications for the development of conservation strategies to protect its genetic diversity. Using 16 microsatellite markers, we genotyped individuals from 20 populations of P. filiformis from across its geographical range and one population of Physaria gracilis for comparison and analyzed genetic diversity and structure. Populations of P. filiformis showed comparable levels of genetic diversity to its congener, except a single population in northwest Arkansas showed evidence of a genetic bottleneck and two populations in the Ouachita Mountains of Arkansas showed lower genetic variation, consistent with genetic drift. Populations showed isolation by distance, indicating that migration is geographically limited, and analyses of genetic structure grouped individuals into seven geographically structured genetic clusters, with geographic location/spatial separation showing a strong influence on genetic structure. At least one population is protected for all genetic clusters except one in north-central Arkansas, which should therefore be prioritized for protection. Populations in the Ouachita Mountains were genetically divergent from the rest of P. filiformis; future morphological analyses are needed to identify whether it merits recognition as a new, extremely rare species.

scholarly journals Analysis of the Association Between TERC and TERT Genetic Variation and Leukocyte Telomere Length and Human Lifespan—A Follow-Up Study

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 82 ◽  
Author(s):  
Daniela Scarabino ◽  
Martina Peconi ◽  
Franca Pelliccia ◽  
Rosa Maria Corbo
Keyword(s):  
Genetic Variation ◽  
Telomere Length ◽  
Elderly Subjects ◽  
Mortality Data ◽  
Leukocyte Telomere Length ◽  
Age Classes ◽  
Follow Up Study ◽  
Human Lifespan ◽  
The Difference

We investigated the possible influence of TERC and TERT genetic variation and leukocyte telomere length (LTL) on human lifespan. Four polymorphisms of TERT and three polymorphisms of TERC were examined in a sample of elderly subjects (70–100 years). After nine years of follow-up, mortality data were collected, and sub-samples of long-lived/not long-lived were defined. TERT VNTR MNS16A L/L genotype and TERT rs2853691 A/G or G/G genotypes were found to be associated with a significantly higher risk to die before the age of 90 years, and with a significantly lower age at death. The association between lifespan and LTL at baseline was analyzed in a subsample of 163 subjects. Age at baseline was inversely associated with LTL (p < 0.0001). Mean LTL was greater in the subjects still living than in those no longer living at follow-up (0.79 T/S ± 0.09 vs 0.63 T/S ± 0.08, p < 0.0001). Comparison of age classes showed that, among the 70–79-year-olds, the difference in mean LTL between those still living and those no longer living at follow-up was greater than among the 80–90-year-olds. Our data provide evidence that shorter LTL at baseline may predict a shorter lifespan, but the reliability of LTL as a lifespan biomarker seems to be limited to a specific age (70–79 years).

scholarly journals Patterns of genetic variation in European plant species depend on altitude

2020 ◽  
Vol 27 (1) ◽  
pp. 157-163
Author(s):  
Christoph Reisch ◽  
Sergey Rosbakh
Keyword(s):  
Genetic Variation ◽  
Plant Species

Mapping genes for growth rate and fatness in a Large White x Meishan F2 pig population

1998 ◽  
Vol 1998 ◽  
pp. 7-7 ◽  
Author(s):  
G.A. Walling ◽  
A.L Archibald ◽  
P.M. Visscher ◽  
C.S. Haley
Keyword(s):  
Growth Rate ◽  
Genetic Variation ◽  
Experimental Design ◽  
Statistical Methods ◽  
Population Based ◽  
Genetic Maps ◽  
Large White ◽  
Backcross Population ◽  
Livestock Species ◽  
Reproduction Traits

DNA-based markers and genetic maps of major livestock species have been developed in the last few years. These, together with experimental populations and appropriate statistical methods, provide the tools to dissect causes of economically important genetic variation in livestock. A cross between genetically diverse lines is a powerful experimental design for such a study. In an F2 or backcross population from such a cross, markers are likely to be highly informative and the genes that control the differences between the lines will be segregating. We have been developing such a resource population based on a cross between the British Large White and Chinese Meishan pigs. These breeds differ for many traits, with the Meishan being inferior for growth rate and fatness, but superior for reproduction traits. Here we report the mapping of major genetic effects on growth rate and fatness in our cross.

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