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.
Highlights
Rye (Secale cereale L.) is one of the most important cereals in Eastern, Central and Northern European countries
The aims of the present study were the following: (1) to characterize a broad collection of rye diverse inbred lines representing the variability among Polish breeding materials with respect to brown rust resistance, pre-harvest sprouting and α-amylase activity, (2) to identify SNPs in ScBx genes and DArTSeq markers associated with these traits
The plant material used in the experiments consisted of 153 diverse inbred lines (DILs) bred in two Polish breeding companies—Danko Plant Breeders Ltd. (40 DILs, designated as D1–D40) and Poznań Plant Breeders Ltd. (30 lines, designated as P1–P30); Botanical Garden of Polish Academy of Science (8 lines; OG1–OG8); Warsaw University of Life Sciences, Department of Plant Genetics, Breeding and Biotechnology (5 lines designated as W1–W5); West Pomeranian University of Technology, Department of Plant Genetics, Breeding and Biotechnology (20 lines designated as S1–S20); and Wrocław University of Environmental and Life Sciences, Department of Genetics, Plant Breeding and Seed Production (50 lines designated as WR1–WR50)
Summary
Rye (Secale cereale L.) is one of the most important cereals in Eastern, Central and Northern European countries. It was grown on approximately 5.8 million ha worldwide in 2013 [http:// faostat.fao.org] Its importance results both from the unique properties such as low water and soil fertility requirements and good tolerance for biotic and abiotic stresses, good overwintering, high nutritional value connected with the content of dietary fibre and the multipurpose usage—for bread making, animal feed and alcohol production. Modern rye varieties do not always exhibit a satisfactory level of resistance to brown rust (Solodukhina 1997; Miedaner et al 2002; Roux et al 2004). This problem, in particular, concerns the population varieties which dominate in Poland. It is known as non-isolatespecific or partial resistance as the disease development is reduced but not completely stopped
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