Abstract
The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.
Highlights
IntroductionObjective of the StudyThe main aim of the study was to establish the localization of an unknown rye gene causing the waxless plant character (Figure 1) on a novel, high density genetic map constructed with DArTseq (sequencing-based diversity array technology) used for genotyping the biparental F2 population
Objective of the StudyThe main aim of the study was to establish the localization of an unknown rye gene causing the waxless plant character (Figure 1) on a novel, high density genetic map constructed with DArTseq used for genotyping the biparental F2 population
The research was based on the standard approach to linkage genetic mapping methods in combination with Machine Learning (ML) to find markers closely linked to the gene of interest
Summary
Objective of the StudyThe main aim of the study was to establish the localization of an unknown rye gene causing the waxless plant character (Figure 1) on a novel, high density genetic map constructed with DArTseq (sequencing-based diversity array technology) used for genotyping the biparental F2 population. The research was based on the standard approach to linkage genetic mapping methods in combination with ML (three algorithms) to find markers closely linked to the gene of interest (putative candidate genes). Plant WaxesThe surface of primary above-ground plant organs is covered with a cuticle, a protective lipid structure sealing the tissues and insulating them from the effects of various unfavorable environmental factors. The cuticle serves as the major barrier preventing nonstomatal water loss and helps to protect plant surfaces from pathogens and ultraviolet radiation [1]. The waxes are either deposited within the cutin matrix (intracuticular wax) or accumulate on its surface as epicuticular wax [2]
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