Refinement of rice blast disease resistance QTLs and gene networks through meta-QTL analysis.

Rice blast disease is the most devastating disease constraining crop productivity. Vertical resistance to blast disease is widely studied despite its instability. Clusters of genes or QTLs conferring blast resistance that offer durable horizontal resistance are important in resistance breeding. In this study, we aimed to refine the reported QTLs and identify stable meta-QTLs (MQTLs) associated with rice blast resistance. A total of 435 QTLs were used to project 71 MQTLs across all the rice chromosomes. As many as 199 putative rice blast resistance genes were identified within 53 MQTL regions. The genes included 48 characterized resistance gene analogs and related proteins, such as NBS-LRR type, LRR receptor-like kinase, NB-ARC domain, pathogenesis-related TF/ERF domain, elicitor-induced defense and proteins involved in defense signaling. MQTL regions with clusters of RGA were also identified. Fifteen highly significant MQTLs included 29 candidate genes and genes characterized for blast resistance, such as Piz, Nbs-Pi9, pi55-1, pi55-2, Pi3/Pi5-1, Pi3/Pi5-2, Pikh, Pi54, Pik/Pikm/Pikp, Pb1 and Pb2. Furthermore, the candidate genes (42) were associated with differential expression (in silico) in compatible and incompatible reactions upon disease infection. Moreover, nearly half of the genes within the MQTL regions were orthologous to those in O. sativa indica, Z. mays and A. thaliana, which confirmed their significance. The peak markers within three significant MQTLs differentiated blast-resistant and susceptible lines and serve as potential surrogates for the selection of blast-resistant lines. These MQTLs are potential candidates for durable and broad-spectrum rice blast resistance and could be utilized in blast resistance breeding.

Androgenesis in indica rice: A comparative competency in development of doubled haploids.

Rice is critical to global food security which demands immediate attention to meet the ever-growing population. Development of improved variety is the major focus area of research, in which doubled haploid (DH) technology plays a vital role. Since, androgenesis shows its potential in DH production, this method was not capitalized specially in indica rice due to due to its recalcitrant nature to tissue culture. Success of androgenesis is governed by many important factors such as stage of anther, pre-treatment conditions, accurate concentrations of media, and plant growth regulators. Though reports of androgenesis are abundant in rice, most of them either used japonica or a specific cultivar of indica rice ecotypes. In this study, a media combination was established which is successful in producing doubled haploids from F1s of Savitri x Pokkali, IR20 x Mahulata along with the popular indica hybrids of Arize 8433DT, Arize 6453, Arize Bold, and Swift Gold. Out of 12 different media combinations tested, and 5 different durations of cold-treatments studied, N6 media with 2,4-D (2.0 mg/l) and BAP (0.5 mg/l) with 7th day cold pre-treatment was found to be most effective in all of the F1s for callus induction. Among all the F1s, rice hybrid, Arize 8433DT showed highest of 52% callus induction. In case of green shoot regeneration, MS media with NAA (0.5 mg/l), BAP (2.0 mg/l) and Kn (1.0 mg/l) (MS+C4) was found to be the most efficient of six treatments studied with highest of 58.25% regeneration in Arize 8433DT. Further, MS+C4 in combination with proline (5.0 mg/l) increased the regeneration rate to 85.99%. Besides, MS media with NAA (1.0 mg/l), Kn (0.1 mg/l) and 50 g/l sucrose was found to be most efficient for supporting root induction in all F1s. This study claims the establishment of genotype independent androgenic protocol for indica rice which could be capitalized in indica rice improvement.