Clavibacter michiganensis (Cm) is a tomato phytopathogenic bacterium. Outbreaks of Cm can result in severe yield and economic losses. To date, no resistance to Cm has been identified. Screening of wild tomato accessions has resulted in the identification of several sources of tolerance to Cm. The genetic background of tolerance provided by these sources is polygenic and complex. Previous results from advanced lines of a cross between Solanum arcanum LA2157 and S. lycopersicum showed that introgression lines carrying a locus of S. arcanum LA2157 on chromosome 7 had high levels of tolerance to Cm. We set out to functionally characterize this locus, in an effort to identify the gene(s) underlying the observed tolerance. Testing of near isogenic lines (NILs) containing a fixed LA2157 introgression on chromosome 7 did not lead to the expected results, as high susceptibility was observed in some NILs homozygous for the S. arcanum LA2157 allele. Therefore, we employed whole genome sequencing in combination with a bulk segregant analysis to identify loci involved in the observed tolerant phenotype. Our results suggest that two additional loci on chromosomes 2 and 4 together with the locus on chromosome 7 are required for tolerance to Cm.

Understanding genetic relationships of maize inbred lines before integrating them into a breeding program is crucial for optimizing heterosis. In this study we assessed the genetic diversity and population structure of 188 early maturing provitamin A maize inbred lines sourced from CIMMYT and IITA using 3.3 K SNPs markers and phenotypic traits data. The results showed highly significant statistical variability (p < 0.000) for key phenotypic traits such as, anthesis date (AD), anthesis-silking interval (ASI), senescence (SEN), ears per plant (EPP) and grain yield (GYD). Inbred lines DS19753, TZMI1989, DS197-206 and DS197-338 had high grain yield under drought and heat stress conditions whilst CML 486, DS197-308, DS197-185, and DS197-318 performed better under non-drought and heat stress conditions. The genetic diversity analysis revealed moderate genetic diversity (GD) of 0.24, and a polymorphic information content (PIC) of 0.20. A minor allele frequency (MAF) of 18% suggested relatively low genetic variation amongst the inbred lines whilst observed heterozygosity (Ho) of 0.02 and Fixation Index (F) of 0.90 indicated fixation of most loci in the inbred lines. Delta K was highest at K = 2 suggesting presence of two distinct genetic sub-populations. Analysis of Molecular Variance indicated that the estimated variance amongst the two populations (0.001) was minimal whilst most of the genetic variance occurs within populations (0.499). The phenotypic diversity revealed supported by genotypic variations among the assessed genotypes suggests a possibility of successful selection of superior drought and heat tolerant provitamin A maize inbred lines that can be used for developing hybrids.