Identification of a candidate gene for the wheat endopeptidase Ep-D1 locus and two other STS markers linked to the eyespot resistance gene Pch1

Abstract

Hansen, Jennifer L.; Zemetra, Robert S.; Santra, Dipak K.; Campbell, Kimberly G.; and Riera-Lizarazu, Oscar, "Identification of a candidate gene for the wheat endopeptidase Ep-D1 locus and two other STS markers linked to the eyespot resistance gene Pch1" (2008 Abstract Wheat is prone to strawbreaker foot rot (eyespot), a fungal disease caused by Oculimacula yallundae and O. acuformis. The most eVective source of genetic resistance is Pch1, a gene derived from Aegilops ventricosa. The endopeptidase isozyme marker allele Ep-D1b, linked to Pch1, has been shown to be more eVective for tracking resistance than DNA-based markers developed to date. Therefore, we sought to identify a candidate gene for Ep-D1 as a basis for a DNA-based marker. Comparative mapping suggested that the endopeptidase loci Ep-D1 (wheat), enp1 (maize), and Enp (rice) were orthologous. Since the product of the maize endopeptidase locus enp1 has been shown to exhibit biochemical properties similar to oligopeptidase B puriWed from E. coli, we reasoned that Ep-D1 may also encode an oligopeptidase B. Consistent with this hypothesis, a sequence-tagged-site (STS) marker, Xorw1, derived from an oligopeptidase B-encoding wheat expressed-sequence-tag (EST) showed complete linkage with Ep-D1 and Pch1 in a population of 254 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Coda and Brundage. Two other STS markers, Xorw5 and Xorw6, and three microsatellite markers (Xwmc14, Xbarc97, and Xcfd175) were also completely linked to Pch1. On the other hand, Xwmc14, Xbarc97, and Xcfd175 showed recombination in the W7984 £ Opata85 RIL population suggesting that recombination near Pch1 is reduced in the Coda/Brundage population. In a panel of 44 wheat varieties with known eyespot reactions, Xorw1, Xorw5, and Xorw6 were 100% accurate in predicting the presence or absence of Pch1 whereas Xwmc14, Xbarc97, and Xcfd175 were less eVective. Thus, linkage mapping and a germplasm survey suggest that the STS markers identiWed here should be useful for indirect selection of Pch1.

Mapping QTL for resistance to eyespot of wheat in Aegilops longissima

“…With the same approach, Leonard et al (2008) linked markers to eyespot resistance gene Pch1 and a major QTL conferring resistance to eyespot on chromosome 5A of Cappelle Desprez was detected (Burt et al 2011). In our study, four QTL conferring resistance to O. yallundae were mapped in the genome of Ae.…”

“…Chao et al (1989) mapped RFLP marker, psr121, at the same location as EP-D1b. Three sequence-tagged-site (STS) markers (orw1, orw5, and orw6) and three microsatellite markers (wmc14, barc97, and cfd175) were tightly linked to Pch1 (Leonard et al 2008). Chapman et al (2008) also found that markers wmc14, barc97, and psr121 were closely linked with Pch1.…”

Discovering Fragrance Biosynthesis Genes from Vanda Mimi Palmer Using the Expressed Sequence Tag (EST) Approach

“…Besides EST-SSR, there are other alternative data mining techniques such as expressed sequence tag-single nucleotide polymorphism (EST-SNP) in maize (Batley et al, 2003), barley (Varshney et al, 2007), melon (Deleu et al, 2009), citrus (Jiang et al, 2010), and cocoa (Allegre et al, 2011), expressed sequence tag-rapid amplified polymorphic DNA (EST-RAPD) in oil palm (Balakrishnan & Vadivel, 2012), and expressed sequence tag-sequence tagged site (EST-STS) in wheat (Leonard et al, 2008;Naji et al, 2008). All the aforementioned techniques are useful for functional genetic diversity estimation of GenBank collections and valuable for use in marker-assisted programmes.…”

Eyespot resistance gene Pch1 and methods of study of its effectiveness in wheat cultivars

“…DNA extraction for the PCR analysis was performed using the DNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. PCR conditions were similar as described by Leonard et al (2008) with minor modifications. A 15 µl reaction volume consisted of 25 ng DNA, 1 U Taq polymerase, 1× PCR buffer, 1.7mM MgCl 2 (Qiagen), 0.17mM of each dNTP and 5µM of the primer pair (Generi Biotech, Hradec Králové, Czech Republic).…”

“…Therefore, more user friendly PCR based alternatives have been searched for in multiple studies. Observations putative homoeologous endopeptidases of wheat, rice and maize suggested that Ep-D1 may encode a serine protease, oligopeptidase B from E. coli, which was a starting point for the development of a sequence-tagged-site (STS) marker Xorw1 (Leonard et al 2008). Pch1 and Xorw1 represent the same or tightly linked locus.…”