[Symbol: see text][Symbol: see text][Symbol: see text].

A 1D/2D genome-wide association study strategy was adopted to investigate the genetic systems underlying the reciprocal adaptation of rice (Oryza sativa) and its bacterial pathogen, Xanthomonas oryzae pv. oryzae (Xoo) using the whole-genome sequencing and large-scale phenotyping data of 701 rice accessions and 23 diverse Xoo strains. Forty-seven Xoo virulence-related genes and 318 rice quantitative resistance genes (QR-genes) mainly located in 41 genomic regions, and genome-wide interactions between the detected virulence-related genes and QR genes were identified, including well-known resistance genes/virulence genes plus many previously uncharacterized ones. The relationship between rice and Xoo was characterized by strong differentiation among Xoo races corresponding to the subspecific differentiation of rice, by strong shifts toward increased resistance/virulence of rice/Xoo populations and by rich genetic diversity at the detected rice QR-genes and Xoo virulence genes, and by genome-wide interactions between many rice QR-genes and Xoo virulence genes in a multiple-to-multiple manner, presumably resulting either from direct protein–protein interactions or from genetic epistasis. The observed complex genetic interaction system between rice and Xoo likely exists in other crop–pathogen systems that would maintain high levels of diversity at their QR-loci/virulence-loci, resulting in dynamic coevolutionary consequences during their reciprocal adaptation.

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

Biotic stresses, including diseases, severely affect rice production, compromising producers’ ability to meet increasing global consumption. Understanding quantitative responses for resistance to diverse pathogens can guide development of reliable molecular markers, which, combined with advanced backcross populations, can accelerate the production of more resistant varieties. A candidate gene (CG) approach was used to accumulate different disease QTL from Moroberekan, a blast-resistant rice variety, into Vandana, a drought-tolerant variety. The advanced backcross progeny were evaluated for resistance to blast and tolerance to drought at five sites in India and the Philippines. Gene-based markers were designed to determine introgression of Moroberekan alleles for 11 CGs into the progeny. Six CGs, coding for chitinase, HSP90, oxalate oxidase, germin-like proteins, peroxidase and thaumatin-like protein, and 21 SSR markers were significantly associated with resistance to blast across screening sites. Multiple lines with different combinations, classes and numbers of CGs were associated with significant levels of race non-specific resistance to rice blast and sheath blight. Overall, the level of resistance effective in multiple locations was proportional to the number of CG alleles accumulated in advanced breeding lines. These disease resistant lines maintained tolerance to drought stress at the reproductive stage under blast disease pressure.

Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of bacterial leaf streak (BLS) is one of the most prevalent rice pathogens in lowland ecologies of Asia and Africa. In Africa, BLS has been reported in several countries, including Nigeria, Senegal, Burkina Faso, Mali, and more recently in Burundi, Uganda and Madagascar (Poulin et al. 2015). BLS can survive in crop debris from season to season or on infected seed, and may be transmitted through irrigation water or on seed (Xie and Mew 1998). In September 2016, we conducted a reconnaissance survey in Ahero rice growing area, Kisumu, Kenya. We observed water-soaked translucent lesions and yellow-brown streak symptoms on three popular rice varieties grown in Kisumu: Pishori, BW96 and Komboka, at the vegetative stage when the plants were about 20 cm tall. The field exhibited 30 to 50% incidence, and severity on infected plants ranged from 20 to 60%, based on IRRI standard evaluation system 2013 (IRRI 2013). We collected six rice leaf samples infected with BLS, and bacteria were isolated, from surfaced sterilized (with 70% ethanol) symptomatic leaf discs, by streak-plating bacterial cells released in sterile water on nutrient agar (NA). Yellow-pigmented Xanthomonas-like positive colonies, following colony PCR, were multiplied by re-streaking on Peptone sucrose agar (PSA) medium (sucrose 10 g, peptone 10 g, bacto agar 16 g, distilled water 1,000 ml), supplemented with three antibiotics, actidione 50 mg liter–1, cephalexin 40 mg liter–1, and kasugamycin 20 mg liter–1. PCR was used to amplify 691 bp DNA fragment used for identification of Xoc (Lang et al. 2010). Xoc strain BLS256 from the Philippines was used as a positive control. The expected DNA fragment corresponding to DNA gyrase subunit B (gyrB) gene was obtained from all isolates upon PCR amplification using the primers XgyrB1-F and XgyrB1-R (Poulin et al., 2014). Negative controls (distilled water as the template) did not show any band. Isolated DNA fragments were submitted to Bioneer (www.bioneer.com) for sequencing. Sequence analysis by BLAST search in the GenBank revealed 99% identity to the sequences of gyrB gene of strains CFBP2286, RS105, L8, BXOR1, BLS279 and B8-12 among others. Two isolates were subjected to pathogenicity test on 4-week-old rice cultivars, IR24 and Pishori. Bacterial cultures grown overnight on PSA medium were centrifuged at 4000 rpm for 5 min, washed and resuspended in sterile water at a concentration of A600 = 0.5, and used for pathogenicity tests in the greenhouse using the 5-week-old rice plants. Rice leaves syringe-infiltrated with bacterial cells showed water-soaked lesions with prominent yellow exudates, typical of BLS symptoms. Control plants infiltrated with sterile water remained symptomless. On re-isolation, typical colonies with Xoc morphology were observed, thus fulfilling Koch's postulates. Partial nucleotide sequences (~670 bp) corresponding to gyrB gene from the two strains used for pathogenicity test (named KN_1 and KN_2) were submitted to GenBank (MF284713 and MF284714). The two isolates have also been deposited to Plant Pathology and Plant-Microbe Biology Section, Cornell University, USA. To our knowledge, this is the first report of Xoc in Kenya. Further work on pathogen collection is required to understand the genotypic and geographic distribution of BLS in Kenya.