Analysis of quantitative disease resistance to southern leaf blight and of multiple disease resistance in maize, using near-isogenic lines.

Maize inbred lines NC292 and NC330 were derived by repeated backcrossing of an elite source of southern leaf blight (SLB) resistance (NC250P) to the SLB-susceptible line B73, with selection for SLB resistance among and within backcross families at each generation. Consequently, while B73 is very SLB susceptible, its sister lines NC292 and NC330 are both SLB resistant. Previously, we identified the 12 introgressions from NC250P that differentiate NC292 and NC330 from B73. The goals of this study were to determine the effects of each introgression on resistance to SLB and to two other foliar fungal diseases of maize, northern leaf blight and gray leaf spot. This was achieved by generating and testing a set of near isogenic lines carry single or combinations of just two or three introgressions in a B73 background. Introgressions 3B, 6A, and 9B (bins 3.03-3.04, 6.01, and 9.02-9.03) all conferred significant levels of SLB resistance in the field. Introgression 6A was the only introgression that had a significant effect on juvenile plant resistance to SLB. Introgressions 6A and 9B conferred resistance to multiple diseases.

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population.

Nested association mapping (NAM) offers power to resolve complex, quantitative traits to their causal loci. The maize NAM population, consisting of 5,000 recombinant inbred lines (RILs) from 25 families representing the global diversity of maize, was evaluated for resistance to southern leaf blight (SLB) disease. Joint-linkage analysis identified 32 quantitative trait loci (QTLs) with predominantly small, additive effects on SLB resistance. Genome-wide association tests of maize HapMap SNPs were conducted by imputing founder SNP genotypes onto the NAM RILs. SNPs both within and outside of QTL intervals were associated with variation for SLB resistance. Many of these SNPs were within or near sequences homologous to genes previously shown to be involved in plant disease resistance. Limited linkage disequilibrium was observed around some SNPs associated with SLB resistance, indicating that the maize NAM population enables high-resolution mapping of some genome regions.

Mapping resistance quantitative trait Loci for three foliar diseases in a maize recombinant inbred line population-evidence for multiple disease resistance?

Southern leaf blight (SLB), gray leaf spot (GLS), and northern leaf blight (NLB) are all important foliar diseases impacting maize production. The objectives of this study were to identify quantitative trait loci (QTL) for resistance to these diseases in a maize recombinant inbred line (RIL) population derived from a cross between maize lines Ki14 and B73, and to evaluate the evidence for the presence genes or loci conferring multiple disease resistance (MDR). Each disease was scored in multiple separate trials. Highly significant correlations between the resistances and the three diseases were found. The highest correlation was identified between SLB and GLS resistance (r = 0.62). Correlations between resistance to each of the diseases and time to flowering were also highly significant. Nine, eight, and six QTL were identified for SLB, GLS, and NLB resistance, respectively. QTL for all three diseases colocalized in bin 1.06, while QTL colocalizing for two of the three diseases were identified in bins 1.08 to 1.09, 2.02/2.03, 3.04/3.05, 8.05, and 10.05. QTL for time to flowering were also identified at four of these six loci (bins 1.06, 3.04/3.05, 8.05, and 10.05). No disease resistance QTL was identified at the largest-effect QTL for flowering time in bin 10.03.

Use of selection with recurrent backcrossing and QTL mapping to identify loci contributing to southern leaf blight resistance in a highly resistant maize line.

B73 is a historically important maize line with excellent yield potential but high susceptibility to the foliar disease southern leaf blight (SLB). NC292 and NC330 are B73 near-isogenic lines (NILs) that are highly resistant to SLB. They were derived by repeated backcrossing of an elite source of SLB resistance (NC250P) to B73, with selection for SLB resistance among and within backcross families. The goal of this paper was to characterize the loci responsible for the increased SLB resistance of NC292 and NC330 and to determine how many of the SLB disease resistance quantitative trait loci (dQTL) were selected for in the development of NC292 and NC330. Genomic regions that differentiated NC292 and NC330 from B73 and which may contribute to NC292 and NC330s enhanced SLB resistance were identified. Ten NC250P-derived introgressions were identified in both the NC292 and NC330 genomes of which eight were shared between genomes. dQTL were mapped in two F(2:3) populations derived from lines very closely related to the original parents of NC292 and NC330--(B73rhm1 x NC250A and NC250A x B73). Nine SLB dQTL were mapped in the combined populations using combined SLB disease data over all locations (SLB AllLocs). Of these, four dQTL precisely colocalized with NC250P introgressions in bins 2.05-2.06, 3.03, 6.01, and 9.02 and three were identified near NC250P introgressions in bins 1.09, 5.05-5.06, and 10.03. Therefore the breeding program used to develop NC292 and NC330 was highly effective in selecting for multiple SLB resistance alleles.

An SSR- and AFLP-based genetic linkage map of tall fescue (Festuca arundinacea Schreb.).

Tall fescue (Festuca arundinacea Schreb.) is commonly grown as forage and turf grass in the temperate regions of the world. Here, we report the first genetic map of tall fescue constructed with PCR-based markers. A combination of amplified fragment length polymorphisms (AFLPs) and expressed sequence tag-simple sequence repeats (EST-SSRs) of both tall fescue and those conserved in grass species was used for map construction. Genomic SSRs developed from Festuca x Lolium hybrids were also mapped. Two parental maps were initially constructed using a two-way pseudo-testcross mapping strategy. The female (HD28-56) map included 558 loci placed in 22 linkage groups (LGs) and covered 2,013 cM of the genome. In the male (R43-64) map, 579 loci were grouped in 22 LGs with a total map length of 1,722 cM. The marker density in the two maps varied from 3.61 cM (female parent) to 2.97 (male parent) cM per marker. These differences in map length indicated a reduced level of recombination in the male parent. Markers that revealed polymorphism within both parents and showed 3:1 segregation ratios were used as bridging loci to integrate the two parental maps as a bi-parental consensus. The integrated map covers 1,841 cM on 17 LGs, with an average of 54 loci per LG, and has an average marker density of 2.0 cM per marker. Homoeologous relationships among linkage groups of six of the seven predicted homeologous groups were identified. Three small groups from the HD28-56 map and four from the R43-64 map are yet to be integrated. Homoeologues of four of those groups were detected. Except for a few gaps, markers are well distributed throughout the genome. Clustering of those markers showing significant segregation distortion (23% of total) was observed in four of the LGs of the integrated map.

Tall fescue EST-SSR markers with transferability across several grass species.

Tall fescue (Festuca arundinacea Schreb.) is a major cool season forage and turf grass in the temperate regions of the world. It is also a close relative of other important forage and turf grasses, including meadow fescue and the cultivated ryegrass species. Until now, no SSR markers have been developed from the tall fescue genome. We designed 157 EST-SSR primer pairs from tall fescue ESTs and tested them on 11 genotypes representing seven grass species. Nearly 92% of the primer pairs produced characteristic simple sequence repeat (SSR) bands in at least one species. A large proportion of the primer pairs produced clear reproducible bands in other grass species, with most success in the close taxonomic relatives of tall fescue. A high level of marker polymorphism was observed in the outcrossing species tall fescue and ryegrass (66%). The marker polymorphism in the self-pollinated species rice and wheat was low (43% and 38%, respectively). These SSR markers were useful in the evaluation of genetic relationships among the Festuca and Lolium species. Sequencing of selected PCR bands revealed that the nucleotide sequences of the forage grass genotypes were highly conserved. The two cereal species, particularly rice, had significantly different nucleotide sequences compared to the forage grasses. Our results indicate that the tall fescue EST-SSR markers are valuable genetic markers for the Festuca and Lolium genera. These are also potentially useful markers for comparative genomics among several grass species.