Fine mapping of the genetic locus <i>L1</i> conferring black pods using a chromosome segment substitution line population of soybean

Abstract

Abstract The colour of plant organs is a useful trait in crop breeding. The pod colours of soybeans primarily include black, brown and tan types, which are controlled by two classical genetic loci, L1 and L2 . Most wild soybeans have black pods, which reflect a possible role in adaptation to the natural environment. Here, an improved chromosome segment substitution line ( CSSL ) population Soja CSSLP 3 was established to identify the L1 gene. The segment on the 19th chromosome represented by the SSR marker Satt313 was found to link with locus L1 . The region was further delimited three times with increased SSR and InDel markers using a population derived from a heterozygous plant of CSSL 124 from Soja CSSLP 3 . The L1 gene was finally located in a 184.43‐kb region between SSR _19p09 and Indel_19P7. Thirteen putative genes in this region were analysed with q RT ‐ PCR . The expression level of Glyma19 g27460, which is a member of the SANT superfamily with a MYB DNA ‐binding domain, was significantly upregulated in black pods and was recognized to be the most likely candidate for the L1 gene.