Query (optional)   in Class  All Allele Author Colleague Collection Assembly Gene Gene Class Gene Product Germplasm Image Journal Keyword Library Locus Map Map Data Marker Pathology Polymorphism Probe Protein QTL Rearrangement Reference Sequence Species Trait Trait Study Two Point Data  

---

GrainGenes Reference Report: TPG-15:e20193

[Submit comment/correction]

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	[ Hide all but 1 of 498 ] WRC1912 WRC1395 WRC1724 WRC1397 WRC0017 WRC1398 WRC1726 WRC0023 WRC0026 WRC1728 WRC1954 WRC0037 WRC1399 WRC1400 WRC1402 WRC1403 WRC0047 WRC1404 WRC2032 WRC1957 WRC0057 WRC1406 WRC1730 WRC0066 WRC1408 WRC2139 WRC0074 WRC2034 WRC1409 WRC2036 WRC1689 WRC1913 WRC0090 WRC0091 WRC0095 WRC2140 WRC0099 WRC1416 WRC1417 WRC0105 WRC0108 WRC0110 WRC1418 WRC0114 WRC2142 WRC2143 WRC1734 WRC0122 WRC1420 WRC0126 WRC1960 WRC0131 WRC1422 WRC1736 WRC0138 WRC0139 WRC1424 WRC1600 WRC1425 WRC1427 WRC0150 WRC0151 WRC2144 WRC2145 WRC0152 WRC0155 WRC0159 WRC0161 WRC1428 WRC2147 WRC1429 WRC2148 WRC2149 WRC0170 WRC1330 WRC2151 WRC0171 WRC2038 WRC2039 WRC1432 WRC1433 WRC0180 WRC0184 WRC1737 WRC1601 WRC1435 WRC1602 WRC1738 WRC2131 WRC0196 WRC0197 WRC0199 WRC1740 WRC1439 WRC1441 WRC2043 WRC2044 WRC1606 WRC1443 WRC1607 WRC1444 WRC0219 WRC1445 WRC0222 WRC0223 WRC0225 WRC0226 WRC1446 WRC0229 WRC2133 WRC1448 WRC0236 WRC2047 WRC2048 WRC1609 WRC2051 WRC2052 WRC2054 WRC2055 WRC2059 WRC2060 WRC2061 WRC0256 WRC1453 WRC0260 WRC2062 WRC1745 WRC0263 WRC1746 WRC0271 WRC1455 WRC1747 WRC0276 WRC0277 WRC0281 WRC2064 WRC1977 WRC0290 WRC1457 WRC1978 WRC1751 WRC0301 WRC1752 WRC0307 WRC1754 WRC1911 WRC1461 WRC1618 WRC1755 WRC1463 WRC1464 WRC1465 WRC1756 WRC1466 WRC1757 WRC0330 WRC1758 WRC1468 WRC1846 WRC1847 WRC2066 WRC1980 WRC1981 WRC1471 WRC1761 WRC1271 WRC2154 WRC0350 WRC0352 WRC0358 WRC2155 WRC0360 WRC2070 WRC1762 WRC1472 WRC1623 WRC0364 WRC0367 WRC1473 WRC0371 WRC1117 WRC0373 WRC2137 WRC2156 WRC0376 WRC1624 WRC1763 WRC0384 WRC1475 WRC1984 WRC1627 WRC1477 WRC1852 WRC1853 WRC0399 WRC0401 WRC2071 WRC2072 WRC0405 WRC1478 WRC1986 WRC1629 WRC1695 WRC0411 WRC1480 WRC1767 WRC1481 WRC1482 WRC0419 WRC1483 WRC1987 WRC1696 WRC2073 WRC2074 WRC1484 WRC1988 WRC0433 WRC1854 WRC1855 WRC1632 WRC1633 WRC0443 WRC1487 WRC1990 WRC1698 WRC1772 WRC1699 WRC1489 WRC1357 WRC1857 WRC0460 WRC1491 WRC1492 WRC1493 WRC2078 WRC2080 WRC1494 WRC1993 WRC0472 WRC1359 WRC1495 WRC0477 WRC1637 WRC2084 WRC1777 WRC1639 WRC1499 WRC0488 WRC1995 WRC1996 WRC1500 WRC0492 WRC0494 WRC1501 WRC1502 WRC1997 WRC0498 WRC2158 WRC2159 WRC0503 WRC1780 WRC1998 WRC0509 WRC1781 WRC1700 WRC1782 WRC1367 WRC0516 WRC1506 WRC1784 WRC1313 WRC1314 WRC1315 WRC1316 WRC2087 WRC2088 WRC1507 WRC1701 WRC1702 WRC0531 WRC0532 WRC1508 WRC1509 WRC1703 WRC0542 WRC0544 WRC1999 WRC1704 WRC2000 WRC0553 WRC1370 WRC0558 WRC1787 WRC1788 WRC2090 WRC1646 WRC1647 WRC1514 WRC1515 WRC1791 WRC1516 WRC1793 WRC0578 WRC0580 WRC1519 WRC1866 WRC1521 WRC2005 WRC1522 WRC1523 WRC2006 WRC1524 WRC2094 WRC1649 WRC0607 WRC1526 WRC1650 WRC1798 WRC0614 WRC2095 WRC2096 WRC1528 WRC2009 WRC0621 WRC0623 WRC1651 WRC1800 WRC1531 WRC1532 WRC1533 WRC1534 WRC1652 WRC0646 WRC1803 WRC0653 WRC1804 WRC1537 WRC1859 WRC0665 WRC0668 WRC0672 WRC0676 WRC0679 WRC2161 WRC0683 WRC0686 WRC0688 WRC1540 WRC1541 WRC0698 WRC1658 WRC0703 WRC1155 WRC1659 WRC1542 WRC2097 WRC2098 WRC0710 WRC0711 WRC1543 WRC2011 WRC1809 WRC1661 WRC1544 WRC1810 WRC1868 WRC1869 WRC1545 WRC0729 WRC0731 WRC1546 WRC2099 WRC2100 WRC1547 WRC2162 WRC2163 WRC0737 WRC1707 WRC1549 WRC0747 WRC1162 WRC0750 WRC2014 WRC1812 WRC1813 WRC0760 WRC1552 WRC1708 WRC1666 WRC1211 WRC0769 WRC0771 WRC2164 WRC1667 WRC1668 WRC1556 WRC1557 WRC0789 WRC2166 WRC1558 WRC1670 WRC1559 WRC0801 WRC0804 WRC0808 WRC1671 WRC2019 WRC1894 WRC2101 WRC0811 WRC0814 WRC0816 WRC1871 WRC0820 WRC0825 WRC0827 WRC1817 WRC1818 WRC1562 WRC0832 WRC1819 WRC1709 WRC0844 WRC0845 WRC0847 WRC0852 WRC1176 WRC1674 WRC1860 WRC1822 WRC1567 WRC1823 WRC1568 WRC0871 WRC1569 WRC0880 WRC1824 WRC1677 WRC1710 WRC0886 WRC1679 WRC1711 WRC1573 WRC1382 WRC1574 WRC1575 WRC1826 WRC0902 WRC1577 WRC2106 WRC2022 WRC2107 WRC1682 WRC1580 WRC0913 WRC0916 WRC0918 WRC1581 WRC1582 WRC2024 WRC0923 WRC1583 WRC0926 WRC0932 WRC1830 WRC1584 WRC0938 WRC0939 WRC2169 WRC1392 WRC0949 WRC1586 WRC1899 WRC2109 WRC0952 WRC0954 WRC0957 WRC1587 WRC2027 WRC1684 WRC1833 WRC2028 WRC1589 WRC0972 WRC1713 WRC1590 WRC1834 WRC0980 WRC2110 WRC0984 WRC0986 WRC1591 WRC0992 WRC1592 WRC0997 WRC1900 WRC2029 WRC1593
Probe	WRC1912_KASP [ Show all 498 ]

GrainGenes is a product of the Agricultural Research Service of the US Department of Agriculture.