Development and validation of a robust KASP marker for zt2 locus in faba bean (Vicia faba)

Abstract

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.

A bHLH transcription factor (VfTT8) underlieszt2, the locus determining zero tannin content in faba bean (Vicia faba L.)

“…Previous studies ascribed this locus to the distal part of chr. III 26,28,29 . The last authors also reported a KASP marker (SNP marker Vf_Mt7g100500_001), 10.5 cM far from flower colour, as a successful marker to discriminate low tannin plants although the closest flanking marker (Vf_Mt1g072740_001), 3 cM apart, failed to distinguish contrasted genotypes in the validation panel 29 .…”

“…III 26,28,29 . The last authors also reported a KASP marker (SNP marker Vf_Mt7g100500_001), 10.5 cM far from flower colour, as a successful marker to discriminate low tannin plants although the closest flanking marker (Vf_Mt1g072740_001), 3 cM apart, failed to distinguish contrasted genotypes in the validation panel 29 . Contradicting the previous report, in this study Vf_Mt7g100500 revealed the highest number of misclassified individuals in any of the faba bean populations assayed preventing it use in marker assisted breeding.…”

“…In pea, the absence of pigmentation in the flower is the result of mutations in loci A and A2 encoding a bHLH transcription factor and a WD40 protein, respectively 21 . A single recessive gene (tan) that encodes a bHLH transcription factor, homologous to the A gene in pea 22 controls white flower in lentils, while in faba bean a WD40 transcription factor (VfTTG1) has been reported as the gene encoding the zt1 phenotypes 26,28,29 .…”

The bHLH transcription factor VfTT8 underlies zt2, the locus determining zero tannin content in faba bean (Vicia faba L.)

“…However, although several studies assigned the locus zt2 to the distal part of chr. III 26,28,29 , the responsible gene is still unknown. More recently, the latter authors 29 reported that a KASP (Kompetitive Allele-Specific PCR) marker (SNP marker Vf_Mt7g100500_001), located at 10.5 cM from the zt2 locus, could be used as a reliable marker to discriminate low-tannin faba bean plants carrying zt2.…”

“…III 26,28,29 , the responsible gene is still unknown. More recently, the latter authors 29 reported that a KASP (Kompetitive Allele-Specific PCR) marker (SNP marker Vf_Mt7g100500_001), located at 10.5 cM from the zt2 locus, could be used as a reliable marker to discriminate low-tannin faba bean plants carrying zt2. However, the relatively high genetic distance from the zt2 locus bears the risk of false selection, due to possible recombination events.…”