Faba bean has the potential to become a key food and feed protein crop in many areas of the world. The presence of tannins in its seed coat has limited the deployment of this crop as feed and food. The expression of either of the two recessive genes, zt1and zt2, causes a great reduction of tannins from the seed coat and results in a white flower phenotype. Molecular markers linked to these loci are fundamental tools for speeding up the breeding of low-tannin varieties. The main aim of this study was to develop and validate a robust molecular marker linked to the zt2 locus. We used 176 recombinant inbred lines of the Disco/2 × ILB 938/2 cross at F 6 and genotyped those using 257 SNP (single nucleotide polymorphism) markers. An SNP marker associated with zt2 locus was found on faba bean chromosome 3 and was used to develop a high-throughput low-cost KASP (kompetitive allele-specific PCR) marker. The KASP marker can successfully discriminate low-tannin faba beans carrying zt2 from those carrying zt1 and wild-type alleles. K E Y W O R D S broad bean, candidate gene, flower colour, molecular breeding, SNP marker, tannins S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Zanotto S, Vandenberg A, Khazaei H. Development and validation of a robust KASP marker for zt2 locus in faba bean (Vicia faba). Plant Breed. 2020;139:375-380. https ://doi.
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Faba
bean is a cool season grain legume that produces seeds with
a high protein content. Seed coat tannins limit its use in food and
feed. A low-tannin phenotype is controlled by either of two unlinked
recessive genes zt1 and zt2. Liquid
chromatography–mass spectrometry was used to characterize phenolic
profiles of seed coat and flower tissue of three faba bean genotypes:
CDC Snowdrop (zt1 gene), Disco/2 (zt2 gene), and ILB 938/2 (tannin-containing). For both tissues, clear
differences in phenolic profiles of ILB 938/2 were observed in comparison
to both low-tannin lines. Although seed coat phenolic profiles of zt1 and zt2 genotypes were similar, distinct
differences were evident in flower tissue, suggesting that the gene
action results in some different end products of the phenolic biosynthetic
pathway. These distinctive compounds could be used as biochemical
markers to distinguish between low-tannin phenotypes.
Improvement of persistency is an important breeding goal in red clover (Trifolium pratense L.). In areas with cold winters, lack of persistency is often due to poor winter survival, of which low freezing tolerance (FT) is an important component. We conducted a genome wide association study (GWAS) to identify loci associated with freezing tolerance in a collection of 393 red clover accessions, mostly of European origin, and performed analyses of linkage disequilibrium and inbreeding. Accessions were genotyped as pools of individuals using genotyping-by-sequencing (pool-GBS), generating both single nucleotide polymorphism (SNP) and haplotype allele frequency data at accession level. Linkage disequilibrium was determined as a squared partial correlation between the allele frequencies of pairs of SNPs and found to decay at extremely short distances (< 1 kb). The level of inbreeding, inferred from the diagonal elements of a genomic relationship matrix, varied considerably between different groups of accessions, with the strongest inbreeding found among ecotypes from Iberia and Great Britain, and the least found among landraces. Considerable variation in FT was found, with LT50-values (temperature at which 50% of the plants are killed) ranging from -6.0°C to -11.5°C. SNP and haplotype-based GWAS identified eight and six loci significantly associated with FT (of which only one was shared), explaining 30% and 26% of the phenotypic variation, respectively. Ten of the loci were found within or at a short distance (<0.5 kb) from genes possibly involved in mechanisms affecting FT. These include a caffeoyl shikimate esterase, an inositol transporter, and other genes involved in signaling, transport, lignin synthesis and amino acid or carbohydrate metabolism. This study paves the way for a better understanding of the genetic control of FT and for the development of molecular tools for the improvement of this trait in red clover through genomics assisted breeding.
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