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GrainGenes Reference Report: TPG-15:e20193

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Reference	TPG-15:e20193
Title	Chromosome-specific KASP markers for detecting Amblyopyrum muticum segments in wheat introgression lines.
Journal	The Plant Genome
Year	2022
Volume	15
Author	Grewal S [ Show all 11 ]
Abstract	Many wild-relative species are being used in prebreeding programs to increase the genetic diversity of wheat (Triticum aestivum L.). Genotyping tools such as single nucleotide polymorphism (SNP)-based arrays and molecular markers have been widely used to characterize wheat–wild relative introgression lines. However, due to the polyploid nature of the recipient wheat genome, it is difficult to develop SNP-based Kompetitive allele-specific polymerase chain reaction (KASP) markers that are codominant to track the introgressions from the wild species. Previous attempts to develop KASP markers have involved both exome- and polymerase chain reaction (PCR)-amplicon-based sequencing of the wild species. But chromosome-specific KASP assays have been hindered by homoeologous SNPs within the wheat genome. This study involved whole genome sequencing of the diploid wheat wild relative Amblyopyrum muticum (Boiss.) Eig and development of a de novo SNP discovery pipeline that generated ~38,000 SNPs in unique wheat genome sequences. New assays were designed to increase the density of Am. muticum polymorphic KASP markers. With a goal of one marker per 60 Mbp, 335 new KASP assays were validated as diagnostic for Am. muticum in a wheat background. Together with assays validated in previous studies, 498 well distributed chromosome-specific markers were used to recharacterize previously genotyped wheat-Am. muticum doubled haploid (DH) introgression lines. The chromosome-specific nature of the KASP markers allowed clarification of which wheat chromosomes were involved with recombination events or substituted with Am. muticum chromosomes and the higher density of markers allowed detection of new small introgressions in these DH lines.
External Databases	https://doi.org/10.1002/tpg2.20193
Locus	WRC1912 [ Show all 498 ]
Probe	[ Hide all but 1 of 498 ] WRC1912_KASP WRC1395_KASP WRC1724_KASP WRC1397_KASP WRC0017_KASP WRC1398_KASP WRC1726_KASP WRC0023_KASP WRC0026_KASP WRC1728_KASP WRC1954_KASP WRC0037_KASP WRC1399_KASP WRC1400_KASP WRC1402_KASP WRC1403_KASP WRC0047_KASP WRC1404_KASP WRC2032_KASP WRC1957_KASP WRC0057_KASP WRC1406_KASP WRC1730_KASP WRC0066_KASP WRC1408_KASP WRC2139_KASP WRC0074_KASP WRC2034_KASP WRC1409_KASP WRC2036_KASP WRC1689_KASP WRC1913_KASP WRC0090_KASP WRC0091_KASP WRC0095_KASP WRC2140_KASP WRC0099_KASP WRC1416_KASP WRC1417_KASP WRC0105_KASP WRC0108_KASP WRC0110_KASP WRC1418_KASP WRC0114_KASP WRC2142_KASP WRC2143_KASP WRC1734_KASP WRC0122_KASP WRC1420_KASP WRC0126_KASP WRC1960_KASP WRC0131_KASP WRC1422_KASP WRC1736_KASP WRC0138_KASP WRC0139_KASP WRC1424_KASP WRC1600_KASP WRC1425_KASP WRC1427_KASP WRC0150_KASP WRC0151_KASP WRC2144_KASP WRC2145_KASP WRC0152_KASP WRC0155_KASP WRC0159_KASP WRC0161_KASP WRC1428_KASP WRC2147_KASP WRC1429_KASP WRC2148_KASP WRC2149_KASP WRC0170_KASP WRC1330_KASP WRC2151_KASP WRC0171_KASP WRC2038_KASP WRC2039_KASP WRC1432_KASP WRC1433_KASP WRC0180_KASP WRC0184_KASP WRC1737_KASP WRC1601_KASP WRC1435_KASP WRC1602_KASP WRC1738_KASP WRC2131_KASP WRC0196_KASP WRC0197_KASP WRC0199_KASP WRC1740_KASP WRC1439_KASP WRC1441_KASP WRC2043_KASP WRC2044_KASP WRC1606_KASP WRC1443_KASP WRC1607_KASP WRC1444_KASP WRC0219_KASP WRC1445_KASP WRC0222_KASP WRC0223_KASP WRC0225_KASP WRC0226_KASP WRC1446_KASP WRC0229_KASP WRC2133_KASP WRC1448_KASP WRC0236_KASP WRC2047_KASP WRC2048_KASP WRC1609_KASP WRC2051_KASP WRC2052_KASP WRC2054_KASP WRC2055_KASP WRC2059_KASP WRC2060_KASP WRC2061_KASP WRC0256_KASP WRC1453_KASP WRC0260_KASP WRC2062_KASP WRC1745_KASP WRC0263_KASP WRC1746_KASP WRC0271_KASP WRC1455_KASP WRC1747_KASP WRC0276_KASP WRC0277_KASP WRC0281_KASP WRC2064_KASP WRC1977_KASP WRC0290_KASP WRC1457_KASP WRC1978_KASP WRC1751_KASP WRC0301_KASP WRC1752_KASP WRC0307_KASP WRC1754_KASP WRC1911_KASP WRC1461_KASP WRC1618_KASP WRC1755_KASP WRC1463_KASP WRC1464_KASP WRC1465_KASP WRC1756_KASP WRC1466_KASP WRC1757_KASP WRC0330_KASP WRC1758_KASP WRC1468_KASP WRC1846_KASP WRC1847_KASP WRC2066_KASP WRC1980_KASP WRC1981_KASP WRC1471_KASP WRC1761_KASP WRC1271_KASP WRC2154_KASP WRC0350_KASP WRC0352_KASP WRC0358_KASP WRC2155_KASP WRC0360_KASP WRC2070_KASP WRC1762_KASP WRC1472_KASP WRC1623_KASP WRC0364_KASP WRC0367_KASP WRC1473_KASP WRC0371_KASP WRC1117_KASP WRC0373_KASP WRC2137_KASP WRC2156_KASP WRC0376_KASP WRC1624_KASP WRC1763_KASP WRC0384_KASP WRC1475_KASP WRC1984_KASP WRC1627_KASP WRC1477_KASP WRC1852_KASP WRC1853_KASP WRC0399_KASP WRC0401_KASP WRC2071_KASP WRC2072_KASP WRC0405_KASP WRC1478_KASP WRC1986_KASP WRC1629_KASP WRC1695_KASP WRC0411_KASP WRC1480_KASP WRC1767_KASP WRC1481_KASP WRC1482_KASP WRC0419_KASP WRC1483_KASP WRC1987_KASP WRC1696_KASP WRC2073_KASP WRC2074_KASP WRC1484_KASP WRC1988_KASP WRC0433_KASP WRC1854_KASP WRC1855_KASP WRC1632_KASP WRC1633_KASP WRC0443_KASP WRC1487_KASP WRC1990_KASP WRC1698_KASP WRC1772_KASP WRC1699_KASP WRC1489_KASP WRC1357_KASP WRC1857_KASP WRC0460_KASP WRC1491_KASP WRC1492_KASP WRC1493_KASP WRC2078_KASP WRC2080_KASP WRC1494_KASP WRC1993_KASP WRC0472_KASP WRC1359_KASP WRC1495_KASP WRC0477_KASP WRC1637_KASP WRC2084_KASP WRC1777_KASP WRC1639_KASP WRC1499_KASP WRC0488_KASP WRC1995_KASP WRC1996_KASP WRC1500_KASP WRC0492_KASP WRC0494_KASP WRC1501_KASP WRC1502_KASP WRC1997_KASP WRC0498_KASP WRC2158_KASP WRC2159_KASP WRC0503_KASP WRC1780_KASP WRC1998_KASP WRC0509_KASP WRC1781_KASP WRC1700_KASP WRC1782_KASP WRC1367_KASP WRC0516_KASP WRC1506_KASP WRC1784_KASP WRC1313_KASP WRC1314_KASP WRC1315_KASP WRC1316_KASP WRC2087_KASP WRC2088_KASP WRC1507_KASP WRC1701_KASP WRC1702_KASP WRC0531_KASP WRC0532_KASP WRC1508_KASP WRC1509_KASP WRC1703_KASP WRC0542_KASP WRC0544_KASP WRC1999_KASP WRC1704_KASP WRC2000_KASP WRC0553_KASP WRC1370_KASP WRC0558_KASP WRC1787_KASP WRC1788_KASP WRC2090_KASP WRC1646_KASP WRC1647_KASP WRC1514_KASP WRC1515_KASP WRC1791_KASP WRC1516_KASP WRC1793_KASP WRC0578_KASP WRC0580_KASP WRC1519_KASP WRC1866_KASP WRC1521_KASP WRC2005_KASP WRC1522_KASP WRC1523_KASP WRC2006_KASP WRC1524_KASP WRC2094_KASP WRC1649_KASP WRC0607_KASP WRC1526_KASP WRC1650_KASP WRC1798_KASP WRC0614_KASP WRC2095_KASP WRC2096_KASP WRC1528_KASP WRC2009_KASP WRC0621_KASP WRC0623_KASP WRC1651_KASP WRC1800_KASP WRC1531_KASP WRC1532_KASP WRC1533_KASP WRC1534_KASP WRC1652_KASP WRC0646_KASP WRC1803_KASP WRC0653_KASP WRC1804_KASP WRC1537_KASP WRC1859_KASP WRC0665_KASP WRC0668_KASP WRC0672_KASP WRC0676_KASP WRC0679_KASP WRC2161_KASP WRC0683_KASP WRC0686_KASP WRC0688_KASP WRC1540_KASP WRC1541_KASP WRC0698_KASP WRC1658_KASP WRC0703_KASP WRC1155_KASP WRC1659_KASP WRC1542_KASP WRC2097_KASP WRC2098_KASP WRC0710_KASP WRC0711_KASP WRC1543_KASP WRC2011_KASP WRC1809_KASP WRC1661_KASP WRC1544_KASP WRC1810_KASP WRC1868_KASP WRC1869_KASP WRC1545_KASP WRC0729_KASP WRC0731_KASP WRC1546_KASP WRC2099_KASP WRC2100_KASP WRC1547_KASP WRC2162_KASP WRC2163_KASP WRC0737_KASP WRC1707_KASP WRC1549_KASP WRC0747_KASP WRC1162_KASP WRC0750_KASP WRC2014_KASP WRC1812_KASP WRC1813_KASP WRC0760_KASP WRC1552_KASP WRC1708_KASP WRC1666_KASP WRC1211_KASP WRC0769_KASP WRC0771_KASP WRC2164_KASP WRC1667_KASP WRC1668_KASP WRC1556_KASP WRC1557_KASP WRC0789_KASP WRC2166_KASP WRC1558_KASP WRC1670_KASP WRC1559_KASP WRC0801_KASP WRC0804_KASP WRC0808_KASP WRC1671_KASP WRC2019_KASP WRC1894_KASP WRC2101_KASP WRC0811_KASP WRC0814_KASP WRC0816_KASP WRC1871_KASP WRC0820_KASP WRC0825_KASP WRC0827_KASP WRC1817_KASP WRC1818_KASP WRC1562_KASP WRC0832_KASP WRC1819_KASP WRC1709_KASP WRC0844_KASP WRC0845_KASP WRC0847_KASP WRC0852_KASP WRC1176_KASP WRC1674_KASP WRC1860_KASP WRC1822_KASP WRC1567_KASP WRC1823_KASP WRC1568_KASP WRC0871_KASP WRC1569_KASP WRC0880_KASP WRC1824_KASP WRC1677_KASP WRC1710_KASP WRC0886_KASP WRC1679_KASP WRC1711_KASP WRC1573_KASP WRC1382_KASP WRC1574_KASP WRC1575_KASP WRC1826_KASP WRC0902_KASP WRC1577_KASP WRC2106_KASP WRC2022_KASP WRC2107_KASP WRC1682_KASP WRC1580_KASP WRC0913_KASP WRC0916_KASP WRC0918_KASP WRC1581_KASP WRC1582_KASP WRC2024_KASP WRC0923_KASP WRC1583_KASP WRC0926_KASP WRC0932_KASP WRC1830_KASP WRC1584_KASP WRC0938_KASP WRC0939_KASP WRC2169_KASP WRC1392_KASP WRC0949_KASP WRC1586_KASP WRC1899_KASP WRC2109_KASP WRC0952_KASP WRC0954_KASP WRC0957_KASP WRC1587_KASP WRC2027_KASP WRC1684_KASP WRC1833_KASP WRC2028_KASP WRC1589_KASP WRC0972_KASP WRC1713_KASP WRC1590_KASP WRC1834_KASP WRC0980_KASP WRC2110_KASP WRC0984_KASP WRC0986_KASP WRC1591_KASP WRC0992_KASP WRC1592_KASP WRC0997_KASP WRC1900_KASP WRC2029_KASP WRC1593_KASP

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