High density SNP genotyping of lines with different storage protein composition reveals sites of interspecific introgression and markers associated with phaseolin or lectin deficiency.

INTRODUCTION: The germplasm lines SARC1, SMARC1-PN1 and SMARC1N-PN1 integrate a progressive deficiency in storage proteins, phaseolin and lectins (Osborn et al. 2003). SARC1 contains arcelin-1 derived from a wild Phaseolus vulgaris accession, G12882. SARC1 had been crossed with MB11-29, lacking phaseolin due to an introgression from P. coccineus and L12-56, lacking major lectins due to an allele from Great Northern 1140. Progeny had been selected giving rise to SMARC1-PN1, lacking phaseolin, and SMARC1N-PN1, lacking both phaseolin and major lectins. The three lines share Sanilac as recurrent background.
MATERIAL AND METHODS: Parental genotypes Sanilac, G12882 and Great Northern 1140, as well as SARC1, SMARC1-PN1 and SMARC1N-PN1 were subjected to high density SNP genotyping using the BARC-Bean6K_3 BeadChip (Song et al. 2015). Also included were three
phaseolin deficient P. coccineus lines (Pandurangan et al. 2016). Parent specific alleles were
identified, and their distribution analyzed among progeny lines.
RESULTS: There were a limited number of P. coccineus specific alleles, present on chromosomes 2, 3, 7 and 11 in SMARC1-PN1 and SMARC1N-PN1 (Figure 1). On chromosome 7, six alleles flank the phaseolin locus, consistent with its introgression from P. coccineus. On chromosome 11, two alleles flank the albumin-1 locus, suggesting a possible origin from the
interspecific parent. A methanol soluble albumin-1 (encoded by Phvul.011G205300.1/-400.1) had been shown to be present at higher levels in SMARC1N-PN1 than SARC1 (Liao et al. 2012). On chromosome 3, another P. coccineus specific allele is proximal to a Great Northern 1140 allele and to a pectin acetylesterase gene (Phvul.003g277600.1) whose transcript was elevated in developing seeds of SMARC1N-PN1 as compared with SARC1 (Liao et al. 2012). G12882 and Great-Northern 1140 specific SNP alleles are linked to the introgression of the
arcelin-phytohemagglutinin-α-amylase inhibitor (APA) locus in SARC1/SMARC1-PN1 versus
SMARC1N-PN1, respectively. The new markers could be useful to breed for bruchid resistance, and provide information on genomic introgression from P. coccineus into P. vulgaris.