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Near-Isogenic Lines for Maize Disease Resistance QTL x Donor Approaches to NIL construction Population of chromosomal segment substitution lines (CSSLs) Recombinant inbred lines (RILs) self Heterogeneous inbred families (HIFs) Introduction: To allow detailed study of quantitative trait loci (QTL), it is necessary to create near isogenic lines (NILs) that differ only for the QTL of interest. In this way, the effects of the QTL can be isolated from other genetic effects. Here we detail the production and analysis to date of NILs that differ for disease resistance QTL. Repeated selfing F1 F1 x Repeated random backcrossing QTL identification Recurrent Parent NILs derived from identified CSSL outliers Marker-assisted backcrossing Backcrossing with recurrent phenotypic selection 38 bins associated with multiple disease resistance QTL were targeted for NIL construction, based on a consensus map of disease QTL in maize (Wisser et al. 2006). HIF- derived NILs were constructed from B73 x CML52 and B73 x DK888. The tropical lines CML52 and DK888 were chosen based on their superior resistance to NLB, GLS, SLB, and other diseases. The NIL pairs are now being characterized for resistance to northern leaf blight (NLB), gray leaf spot (GLS), southern leaf blight (SLB), anthracnose leaf blight (ALB), common rust, and common smut. NILs derived from heterogeneous inbred families (HIFs) Acknowledgements: Funding for this work is from the CGIAR Generation Challenge Program, the USDA Agricultural Research Service (ARS), The McKnight Foundation, and the Corn Growers Association of North Carolina. References: Szalma et al. (2007) Theor. Appl. Genet. 114: 1211-1228. Wisser et al. (2006) Phytopathology 96: 120-129. a The NLB-QTL was identified from corresponding heterogeneous inbred families in 2005 to 2006, but significant phenotypic contrast was not detected in selected NIL pairs at Aurora, 2007. b Data based on one-year field trials, and need to be further validated. (Common rust and common smut are from natural infection.) NILs derived from marker-assisted backcrossing Major SLB QTL SLB QTL Chr. 1 SLB QTL Chr. 3 B73 NIL pairs inoculated with NLB and ASR B73 NILs inoculated with SLB in the field B73 NIL with Chr. 1 introgression B73 NIL with Chr. 3 introgression NILs derived from backcrossing with recurrent phenotypic selection u1228 m0371 Chromosome 4 p072 u1008 b1434 nc135 u1669 u1509 b1126 u2281 p096 b1265 u2054 u1142 u1451 u1896 u2027 u2038 b1189 u1808 u2041 m0321 u2285 u1313 u1999 u1101 b589 b1890 0.0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 Chromosome 1 Chromosome 2 p96100 u2246 u2363 b1017 b1338 m0111 u1756 u1261 u2248 p109642 b1018 m0401 b1831 b1036 b1138 u1080 u2372 b1329 u1042 b1662 b1940 b1520 u1252 p101049 u1696 AY111236 0.0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 Chromosome 3 u2118 u2256 p104127 u1886 b1325 b1523 u1057 u2258 u2369 p099 u2000 u2158 b2047 u2261 u2264 u1773 b1456 b1904 u1920 u2376 u1266 b1449 b1047 u2266 u2269 u2270 u2271 dupssr17 b1605 u1825 m0251 b1108 u1273 u2276 dupssr33 b1182 b1496 u1062 u1594 u1136 0.0 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 Chromosome 5 u1308 u1496 u1781 b105 b1046 u1447 u1355 b1287 b1208 m0081 u1853 u1722 p101 u2216 p048 b2305 b118 AY105910 u2307 0.0 50 100 150 200 250 300 350 400 450 500 550 600 650 Chromosome 10 p041 u1293 u1291 u1152 u2034 u1337 p059 u1863 u1866 p050 u1995 b1526 u1077 u1115 u1506 b1028 u1084 b1360 b1185 50 100 150 200 250 300 350 400 450 0.0 b1065 Chromosome 8 u1414 b1194 u1913 b1834 b1863 u1457 b1176 b666 b1782 b1031 dupssr14 b1056 b1131 0.0 50 100 150 200 250 300 350 400 450 500 550 600 Chromosome 6 b1043 b426 b1371 u1083 u1572 AY111964 m0241 b1732 u1859 p299852 b1740 b1521 b1538 nc009 u2324 0.0 50 100 150 200 250 300 350 400 450 500 Chromosome 7 b1367 b2132 u1159 b1094 u1983 b1022 b1808 b1305 b1070 b1805 b1666 b2259 b1407 p051 0.0 50 100 150 200 250 300 350 400 450 500 550 600 Chromosome 9 800 0.0 50 100 150 200 250 300 350 400 450 500 550 -39.0 700 750 600 650 u1279 b1724 u1867 u2393 b1810 b1583 u2335 u1596 u1430 b244 p061 u1107 u2398 u1120 u1078 u1231 u2095 u2343 u2371 b1191 u1366 b619 b128 u1982 u1277 NC250 Introgression likely derived from B37 NC250 Introgression likely derived from Nigerian Composite ARb NC250 Introgression in both NC292 and NC330 NC250 Introgression in NC292 NC250 Introgression in NC330 Unknown no SSR data Major SLB QTL positions B73/NC250A F 2:3 population umc1704 umc1532 umc2011 bnlg1917 u1636 dupssr19 b2228 u1177 b149 0.0 50 a31 b1429 u1160 b1484 b1866 b652 u2227 b2086 u1297 u1988 u1254 u1035 u1122 u1661 u1358 b1556 b1025 u1128 p037 u1848 m0041 u2047 u1298 u1431 b1671 b1347 u1500 p265454 u1553 u1129 u1118 b2123 u1725 u2244 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1000 1050 1100 u2053 u1576 b594 IDP1471 IDP4016 500 A A B B C C D D E E F F G G H H I I J J K K The sister lines NC292 and NC330 were derived in the 1980s by Don Thompson at NCSU by repeatedly backcrossing a B73 / NC250 hybrid to B73 and selecting for SLB resistance at each generation. The resulting lines are more than 90% B73 genome-derived while retaining much of the original SLB resistance from NC250. We scanned the genomes of NC292 and NC330, and identified the 11 introgressed regions (shown right). We then constructed and tested B73 NILs carrying each of the introgressed regions alone (far right). CSSLs outliers identified The TBBC3 population (Szalma et al. 2007) consists of 90 lines with an average 89% B73 constitution. Each line carries a different set of introgressions from the line Tx303. We screened this population for lines that differed significantly in disease resistance from the B73 recurrent parent lines and from the rest of the population. B73 Tx303 introgression at bin 1.02 Tx303 introgression at bin 1.06 B73 NILs inoculated with NLB in the field B73 NILs infected with GLS in the field B73 Tx303 introgression at bin 1.01 DK888 at bin 8.06 B73 at bin 8.06 B73 NILs inoculated with SLB in the field John Zwonitzer 1* , Chia-Lin Chung 2* , Joy Longfellow 2 , Rebecca Nelson 2 , Peter Balint-Kurti 1 1 USDA-ARS and NCSU Dept. of Plant Path., 2 Cornell University Dept. of Plant Path. *Joint First Authors Regions introgressed B73 Introgression AB Introgression BD Introgression BD Introgression BG Introgression G Introgression K Introgression GH Introgression CFG DK888 No — No No CML52? a No CML52 No CML52 or B73 (epistasis btw QTL in bin 2.10 and 5.03) No CML52? a CML52? a NLB S11 / DK888 B73 / CML52 Cross of origin — — — — — — 8.06 No No S11 b No No — 6.05 No No S11 b No No — 5.06 S11 b No No No DK888 b — 5.04 No No No No No — 3.04 CML52 b No No No No No 8.02/03 NLB, rust No No CML52 b No No No 7.04 SLB, ALB No No CML52 b No No No 6.05 NLB, ALB, rust CML52 b No No No No No 3.06 No No No No No No 2.10, 5.03 SLB No No No No No No 2.04/06 No No No No No No 1.07/08 SLB, ALB No No No No No No 1.06 Smut b Rust b ASR b ALB b SLB b GLS b Differential in resistance, but causative QTL unknown Disease resistance (allele conferring resistance) Contrasting regions in available NIL pairs (bin) B73 at bin 6.05 CML52 at bin 6.05 CML52 at bin 6.05 CML52 NILs contrasting for bin 6.05 DK888 NILs contrasting for bin 8.06 B73 at bin 6.05
