ATP-Dependent Clp Protease Subunit C1, HvClpC1, Is a Strong Candidate Gene for Barley Variegation Mutant luteostrians as Revealed by Genetic Mapping and Genomic Re-sequencing

Abstract

Implementation of next-generation sequencing in forward genetic screens greatly accelerated gene discovery in species with larger genomes, including many crop plants. In barley, extensive mutant collections are available, however, the causative mutations for many of the genes remains largely unknown. Here we demonstrate how a combination of low-resolution genetic mapping, whole-genome resequencing and comparative functional analyses provides a promising path toward candidate identification of genes involved in plastid biology and/or photosynthesis, even if genes are located in recombination poor regions of the genome. As a proof of concept, we simulated the prediction of a candidate gene for the recently cloned variegation mutant albostrians (HvAST/HvCMF7) and adopted the approach for suggesting HvClpC1 as candidate gene for the yellow-green variegation mutant luteostrians.

Homozygosity mapping identified loci and candidate genes responsible for freezing tolerance in Camelina sativa

“…Li et al. (2021) used a modified homozygosity mapping approach to identify the gene underlying the barley variegation mutant luteostrians. However, to our knowledge, the application of homozygosity mapping to identify candidate genes for a non‐mutant trait from a bi‐parental segregating population has not been reported in any plants.…”

“…A schematic for how this works is shown in Figure 1. Although homozygosity mapping is similar to bulk segregant analysis (Li et al., 2021; Michelmore et al., 1991; Wang et al., 2021), it differs in that rather than just selecting two extremes of the population with no regard to genotype, only individuals known to be homozygous for the traits are selected and compared to individuals known to be heterozygous. Also, rather than just looking for statistical associations between markers and the trait of interest, the goal of homozygosity mapping is to identify contiguous stretches of DNA that are homozygous in all individuals that are fixed for the trait, and which are heterozygous in all individuals where the trait is segregating.…”

GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing

“…Data for test analysis. For the test application of the GBS-DP pipeline in the present work, we used project PRJEB39633 from the European Nucleotide Archive (ENA) database (Leinonen et al, 2010), which contains GBS sequencing data for a barley (Hordeum vulgare) population derived from a cross between the six-row barley variety Morex and the mutant line luteostrians-P1 (lst/LST) (Li M. et al, 2021). Libraries were obtained using a combination of MspI and PstI restriction enzymes (Wendler et al, 2015).…”