ABSTRACT

Gene-specific markers linked to major genes controlling a trait will have a major impact in understanding and improvement of the respective traits in an efficient manner. Target region amplification polymorphism (TRAP), an efficient PCR-based marker system, offers a great potential to develop markers targeting candidate gene sequences. Using this marker technique, TRAP markers have been developed for the teosinte branched 1 (tb1) gene (thought to be involved in stress responsive apical dominance in teosinte and pearl millet), and brown midrib 1 (bm1) and brown midrib 3 (bm3) genes (thought to be involved in lignin biosynthesis and straw digestibility in maize, sorghum, and in pearl millet) in pearl millet. While the former gene is a candidate for a major drought tolerance quantitative trait locus (QTL), the latter two genes are candidates for stover yield and quality QTLs. Twenty TRAP marker bands were developed from PCR products of 6 TRAP primer pairs (fixed + arbitrary primer combinations) when visualized using the silver staining procedure for the three genes under study. All 20 TRAP markers were mapped using ‘Mapmaker’ software in a framework linkage map consisting of 31 RFLP, 28 SSR and 19 SSCP-SNP markers on a mapping population (ICMB 841-P3 ´ 863B-P2), which was previously used to map the targeted drought tolerance and stover yield and quality QTLs. Two out of 10 developed TRAP markers for the tb1 target mapped to a major drought tolerance QTL on linkage group 2, similarly, 2 out of 10 developed for the two brown midrib gene targets mapped to a consistent stover quality QTL on linkage group 3, finally resulting in high (20% in this case) efficiency in producing trait specific markers associated with candidate genes.

The TRAP protocol successfully generated trait-specific markers. TRAP markers offer a potentially inexpensive means for preliminary evaluation of candidate genes during development of near-perfect selectable markers for species with limited sequence information.