Bulk segregant analysis (BSA) for improving cold stress resistance in maize using SSR markers

Abstract

ABSTRACT. In this study, eight inbred maize lines with high or low tolerance to cold temperature were investigated using bulk segregant analysis (BSA). Genetic diversity and genetic relationships were investigated using 100 simple sequence repeat (SSR) markers linked to cold tolerance in maize. A total of 319 alleles were identified. Among these, 128 were high coldtolerant-specific alleles and 61 were poorly coldtolerant-specific alleles, while the remaining 130 were shared between the two types. The number of alleles per locus ranged from 2 to 5, with an average of 3.19. The major allele frequency varied from 0.39 to 0.53 with an average of 0.47. The average gene diversity and polymorphic information content among all lines were 0.63 and 0.58, respectively. A dendrogram analysis identified three main clusters and most of the high tolerant inbred lines were clearly distinguished from the poorly tolerant inbred lines. In addition to the BSA, a total of 84 SSR markers were identified as high cold tolerance-specific alleles and 52 SSRs were detected as poorly cold tolerance-specific alleles. Of these, bnlg1273, umc1124, dupssr21, mmc0251, mmc0181, and phi041 have great potential for being molecular markers for cold tolerance in maize. Our results were in agreement with results previously reported for SSR markers linked with cold tolerance in maize. The identification and characterization of high and poorly cold tolerant maize lines based on SSR markers will be useful for future maize breeding studies.

A novel quantitative trait loci governs prolificacy in ‘Sikkim Primitive’ – A unique maize (Zea mays) landrace of North‐Eastern Himalaya

“…(2020) identified a major QTL governing anaerobic germination in rice landrace ‘BJ’ using BSA. Similarly, BSA was used in molecular mapping and tagging of genes governing quantitative traits such as drought tolerance (Gemenet et al., 2010; Quarrie et al., 1999), southern corn leaf blight resistance (Cai et al., 2003), cold stress resistance (Farooqi et al., 2016) and aluminium toxicity tolerance (Ninamango‐Cárdenas et al., 2003) in maize.…”

Genetic loci associated with winter survivorship in diverse lowland switchgrass populations

“…(1991), it has been successfully implemented in several crops for both qualitative and quantitative traits using dominant or codominant markers, mostly in mapping populations. Examples include cold stress resistance in maize ( Zea mays L.) (Farooqi et al., 2016), drought resistance in maize (Quarrie et al., 1999), drought resistance in rice ( Oryza sativa L.) (Salunkhe et al., 2011; Vikram et al., 2012), salt tolerance in rice (Tiwari et al., 2016), Fusarium head blight in wheat ( Triticum aestivum L.) (Shen et al., 2003), xylose utilization from Saccharomyces cerevisiae (Wenger et al., 2010), scab resistance in apple ( Malus domestica Borkh.) (Yang et al., 1997), and cold tolerance in rice (Sun et al., 2018; Takagi et al., 2013).…”

Physiological Analysis and Genetic Mapping of Short Hypocotyl Trait in Brassica napus L.

“…Then, annealing temperature was reduced in each cycle by 1 • C for 8 cycles from 55 • C; the annealing temperature was maintained at 50 • C for the remaining 30 cycles, followed by a final step at 72 • C for 5 min. The amplified PCR products were separated via vertical electrophoresis in 8% polyacrylamide gel in 1 × TBE buffer at a constant 180 V for 1.5 h, visualized with silver staining and captured using a digital camera [50]…”