Molecular characterization of Asian maize inbred lines by multiple laboratories.

This study focuses on the standardization of techniques across laboratories to enable multiple datasets to be compared and combined in order to obtain reliable and robust wide-scale patterns of diversity. A set of protocols using a core collection of simple sequence repeat (SSR) markers, reference lines and standard alleles, plus a common system of allele nomenclature, was adopted in the study of maize genetic diversity in a network of laboratories in Asia. Pair-wise allele comparisons of the reference lines, done to assess the general agreement between datasets from four laboratories, showed error rates (raw) ranging from 5.8% to 9.7%, which were reduced to less than 8% after adjustments of correctable errors, and further reduced to less than 6% after the exclusion of all markers with greater than 10% individual error rates. Overall, 45% of the total mismatches were due to frameshift errors, 39% to wrong allele size, 15% to failed amplification and 1% to "extra" alleles. Higher genetic similarity values of the reference lines were achieved using fewer markers with data of higher quality rather than with more markers of questionable quality. Cluster analysis of the merged datasets showed the lines from southern China to be highly diverse, falling into six of the seven clusters observed and all well represented by tester lines. The lines from Indonesia fell into five of six groups, with two main groups represented by tester lines. The CIMMYT lines developed for the Asian region showed a relatively narrow genetic base, falling in two out of seven and in three out of six clusters in China and Indonesia, respectively. In contrast to the case in southern China where 95% of the lines clustered separately from the CIMMYT lines, lines in the Indonesian breeding program show a closer relationship with the CIMMYT lines, reflecting a long history of germplasm exchange.

Identification of QTLs conferring resistance to downy mildews of maize in Asia.

Downy mildew is one of the most destructive diseases of maize in subtropical and tropical regions in Asia. As a prerequisite for improving downy mildew resistance in maize, we analyzed quantitative trait loci (QTLs) involved in resistance to the important downy mildew pathogens--Peronosclerospora sorghi (sorghum downy mildew) and P. heteropogoni (Rajasthan downy mildew) in India, P. maydis (Java downy mildew) in Indonesia, P. zeae in Thailand and P. philippinensis in the Philippines--using a recombinant inbred line population derived from a cross between Ki3 (downy mildew resistant) and CML139 (susceptible). Resistance was evaluated as percentage disease incidence in replicated field trials at five downy mildew 'hotspots' in the four countries. Heritability estimates of individual environments ranged from 0.58 to 0.75 with an across environment heritability of 0.50. Composite interval mapping was applied for QTL detection using a previously constructed restriction fragment length polymorphism linkage map. The investigation resulted in the identification of six genomic regions on chromosomes 1, 2, 6, 7 and 10 involved in the resistance to the downy mildews under study, explaining, in total, 26-57% of the phenotypic variance for disease response. Most QTL alleles conferring resistance to the downy mildews were from Ki3. All QTLs showed significant QTL x environment interactions, suggesting that the expression of the QTL may be environment-dependent. A strong QTL on chromosome 6 was stable across environments, significantly affecting disease resistance at the five locations in four Asian countries. Simple-sequence repeat markers tightly linked to this QTL were identified for potential use in marker-assisted selection.

Identification of Resistance Genes Effective Against Rice Bacterial Blight Pathogen in Eastern India.

Breeding for bacterial blight resistance in rice requires an understanding of the contemporary pathogen populations in the locations where resistance genes are to be deployed. We characterized 450 strains of Xanthomonas oryzae pv. oryzae collected from three states of India using polymerase chain reaction fingerprinting and virulence analysis. This pathogen collection was differentiated into 17 haplotypes (12 lineages at 80% similarity level). Significant differences in the distribution of haplotypes were observed among regions. Virulence analysis of the pathogen collection revealed nine pathotypes. Among the populations from three regions, the Orissa population was the most diverse, consisting of 11 out of 17 haplotypes and five out of nine pathotypes detected in the total collection. Representative pathotypes were used to evaluate seven near-isogenic lines carrying individual bacterial blight resistance genes (Xa3, Xa4, xa5, Xa7, Xa10, xa13, and Xa21) and gene pyramids. Pathogen strains compatible to individual genes were present in detectable frequencies, although no single strain could overcome all resistance genes. Gene combinations Xa4 + xa5, xa5 + Xa21, and Xa4 + xa5 + Xa21 conferred a broad spectrum of resistance to all the strains evaluated, supporting the strategy of pyramiding appropriate resistance genes.