Seed coat colour of Indian mustard [Brassica juncea (L.) Czern. and Coss.] is associated with Bju.TT8 homologs identifiable by targeted functional markers

Abstract

Seed coat colour is an important trait in Indian mustard. Breeding for seed coat colour needs precise knowledge of mode of inheritance and markers linked to it. The present study was focussed on genetics and development of functional markers for seed coat colour. F1s (direct and reciprocal) and F2populations were developed by crossing two contrasting parents for seed coat colour (DRMRIJ-31, brown seeded and RLC-3, yellow seeded). Phenotypic results have shown that the seed coat colour trait was under the influence of maternal effect and controlled by digenic-duplicate gene action. Further,Bju.TT8homologs of both parents (DRMRIJ-31 and RLC-3) were cloned and sequenced. Sequencing results ofBju.TT8homologs revealed that in RLC-3, geneBju.ATT8had an insertion of 1279bp in the 7thexon; whereas, geneBju.BTT8had an SNP (C→T) in the 7thexon. These two mutations were found to be associated with yellow seed coat colour. Using sequence information, functional markers were developed for bothBju.TT8homologs, validated on F2population and were found highly reliable with no recombination between the markers and the phenotype. Further, these markers were subjected to a germplasm assembly of Indian mustard, and their allelic combination for the seed coat colour genes has been elucidated. The comparative genomics ofTT8genes revealed high degree of similarity between and across theBrassicaspecies, and the respective diploid progenitors in tetraploidBrassicaspecies are the possible donors ofTT8homologs. This study will help in the marker-assisted breeding for seed coat colour, and aid in understanding seed coat colour genetics more precisely.