Identification of Single Nucleotide Polymorphisms Associated with Brown Rust Resistance, α-Amylase Activity and Pre-harvest Sprouting in Rye (Secale cereale L.)

Abstract

Rye is a crop with relatively high resistance to biotic and abiotic stresses. However, the resistance to brown rust (Puccinia recondita f. sp. secalis) and pre-harvest sprouting are still not satisfactory. High α-amylase activity is also among the main disadvantages of this species. Therefore, effective tools, e.g. molecular markers, allowing precise and environmentally independent selection of favourable alleles are desirable. In the present study, two kinds of association mapping—genome-wide association mapping (GWAM) based on sequences of DArTSeq markers and candidate gene association mapping (CGAM) based on sequences of ScBx genes—were chosen for development of molecular markers fulfilling these criteria. The analysed population consisted of 149 diverse inbred lines (DILs). Altogether, 67 and 11 single nucleotide polymorphisms (SNPs) identified in, respectively, GWAM and CGAM, were significantly associated with the investigated traits: 2 SNPs with resistance to brown rust, 71 SNPs with resistance to pre-harvest sprouting and 5 SNPs with α-amylase activity in the grain. Fifteen SNPs were stable across all environments. The highest number (13) of environmentally stable SNPs was associated with pre-harvest sprouting resistance. The test employing the Kompetitive Allele Specific PCR method proved the versatility of four markers identified in both GWAM and CGAM.Electronic supplementary materialThe online version of this article (doi:10.1007/s11105-017-1030-6) contains supplementary material, which is available to authorized users.

Genes ScBx1 and ScIgl—Competitors or Cooperators?

“…Overall, lines L318 and D39 showed the greatest similarity in terms of gene expression and BX profiles. This is in accordance with the values of the Dice similarity coefficient calculated based on data obtained previously [16,43], which were 0.508, 0.523, and 0.546 for pairs D33/D39, D33/L318, and D39/L318, respectively.…”

“…The highest content of BXs was found in line D33, while the lowest one was in line D39. The same relationship was observed in the case of field-grown plants with respect to DIBOA, but not for GDIBOA; line L318 was characterized by the highest content of this BX [43].…”

“…In our previous study, we detected several polymorphisms in the ScBx1 gene associated with the content of BX. At two polymorphic sites, the first one positioned in the gene promoter line and the second one in 3 UTR, lines D33 and D39 possessed the same, "positive" nucleotides, namely, T and G, while line L318 had the "negative" nucleotides G and T, respectively [43].…”

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping‐by‐sequencing

“…Compared to SNP arrays, reduced‐representation sequencing methods based on digestion with restriction enzymes have the advantage of joint discovery and genotyping of sequence variant without the requirement for ascertaining polymorphic markers in a discovery panel, which may lead to underestimation of genetic diversity of diverse genetic material. A flavor of reduced‐representation sequencing, DArTseq (Li et al., ), has been previously employed for linkage mapping in rye (Milczarski, Hanek, Tyrka, & Stojałowski, ; Rakoczy‐Trojanowska et al., ).…”

QTL mapping for benzoxazinoid content, preharvest sprouting, α-amylase activity, and leaf rust resistance in rye (Secale cereale L.)

“…[ 7 ]; this suggests that there is a functional allelic variation in these structural loci. SNP in the Bx genes were also found to be associated with variations of leaf rust resistance and preharvest sprouting (PHS) within a wide collection of genetically diverse rye materials [ 10 ]. This finding raises a question on the possible role of BX production in regulating such important agronomic traits as leaf rust resistance, PHS, and α-amylase activity in rye grain.…”