Breeding for resistance to rice yellow mottle virus and improved yield in rice (oryza sativa L.) in Tanzania.

Abstract

Rice [Oryza sativa (L.), 2n = 2x = 24] is the second most important staple food crop after wheat (Triticum aestivum L.) serving more than half of the world’s population. In Tanzania, rice is the second most important cereal crop after maize (Zea mays L.). However, rice production and productivity in the country is hindered by several factors. One of the leading biotic constraints is the rice yellow mottle virus (RYMV) disease which is devastating the existing rice varieties, and causes severe yield losses of 20 to 100 % under field conditions. Both landraces and introduced varieties that are grown by farmers succumb to RYMV. Several control strategies have been recommended to reduce RYMV infection: however, the development and deployment of RYMV resistant varieties is the most effective, economical and environmentally friendly approach for subsistence farmers. Breeding for resistance to RYMV and improved yields are the main goals for rice breeders aiming to develop and release improved rice cultivars that meet the preferences of the farmers and their markets. Therefore, the objectives of this study were to: (i) assess farmers’ perceptions, production constraints and variety preferences of rice in Tanzania to guide breeding; (ii) determine variation among Tanzanian rice germplasm collections based on agronomic traits and resistance to RYMV to select unique parents for breeding; (iii) assess the genetic diversity and population structure of rice genotypes using simple sequence repeat (SSR) markers to complement phenotypic profile and select parents; and (iv) determine the combining ability and gene action for resistance to RYMV disease and for key agronomic traits in rice, and thereby to develop new populations of parental germplasm for future breeding. A participatory rural appraisal study was conducted involving 180 participants, using a structured questionnaire and focused group discussions with 90 farmers in the Mvomero, Kilombero and Kyela districts of Tanzania. The results indicated that rice was the most important food and cash crop, followed by maize, cassava (Mannihot esculenta Crantz), sweetpotato (Ipomoea batatas [L..] Lam.), sugarcane (Saccharum officinarum L.), pigeonpea (Cajanus cajan L.), cowpea (Vigna unguiculata [L.] Walp.), sesame (Sesamum indicum L.), common bean (Phaseolus vulgaris L.), cocoa (Theobroma cacao L.), banana (Musa acuminate L.), groundnut (Arachis hypogaea L.), and oil palm (Elaeis guineensis Jacq.). The majority of the respondents (67.2%) used farm saved seed from the previous rice harvest. The major constraints limiting rice production and productivity in all studied areas were diseases, insect pests, frequent droughts, the non-availability and high cost of fertilizers, a limited number of improved cultivars, poor soil fertility and bird damage. The farmers preferred rice varieties with high yield, disease resistance, drought tolerance, high market value, early maturity, attractive aroma, and local adaptation. A systematic rice-breeding program aimed

at improving RYMV resistance and incorporating farmers’ preferred traits should be designed and implemented as a means to increase the productivity and adoption of new cultivars by the farmers across the rice-growing areas of Tanzania. Fifty-four rice genotypes were field evaluated at two important rice production sites (Ifakara and Mkindo), which are recognized as RYMV hotspots in Tanzania, using a 6 × 9 alpha lattice design with two replications. There were significant (p<0.05) genotypic variations for agronomic traits and RYMV susceptibility in the tested germplasm. Seven genotypes with moderate to high RYMV resistance identified, namely Salama M-57, SSD1, IRAT 256, Salama M-55, Mwangaza, Lunyuki, and Salama M-19 were identified as new sources of resistance genes. Positive and significant correlations were detected between grain yield and number of panicles per plant (NPP), panicle length (PL), number of grains per panicle (NGP), percentage-filled grains (PFG), and thousand-grain weight (TGW), which are useful traits for simultaneous selection for rice yield improvement. A principal component analysis resulted in five principal components accounting for 79.88% of the total variation present in the assessed germplasm collection. Traits that contributed most to the total genotypic variability included NPP, number of tillers per plant (NT), PL, grain yield (GY), and days to 50% flowering (DFL). Genotypes, Rangimbili, Gigante, and SARO have complementary agronomic traits and RYMV resistance, and can be recommended for further evaluation, genetic analysis and breeding. The genetic relationship and divergence of the 54 rice selected genotypes mentioned above were examined using 14 polymorphic simple sequence repeats (SSR) markers to select unique parents for breeding. Data analysis was based on marker and population genetic parameters. The mean polymorphic information content (PIC) was 0.61, suggesting a high level of polymorphism for the selected SSR markers among the rice accessions. The population structure revealed a narrow genetic base, with only two major sub-populations. Analysis of molecular variance revealed that only 30% of the variation was attributed to population differences, while 47% and 23% were due to variation among individuals within populations and within individual variation, respectively. The genetic distance and identity among genotypes varied from 0.083 to 1.834 and 0.159 to 0.921, respectively. A dendrogram grouped the genotypes into three clusters with wide variation. The selected genetic resources, namely IR56, Mwanza, Salama M-55, Sindano nyeupe, SARO, Gigante, Lunyuki, Rangimbili, IRAT 256, Zambia and Salama M-19, will be useful resources for rice breeding in Tanzania and other African countries because they are genetically diverse. The final study involved combining ability analysis of the above selected genotypes and derived families to assess gene action conditioning RYMV resistance and agronomic traits. Ten parental lines and their 45 F2 progenies were field evaluated at three selected locations using a 5 × 11 alpha lattice design with two replications. The genotype × site interaction effects were significant (p<0.05) for the NT, NPP, NGP, percentage of filled grains (PFG), TGW, rice yellow mottle virus disease (RYMVD) resistance and GY. The variance due to the general combining ability (GCA) and the specific combining ability (SCA) effects were both significant for all assessed traits, indicating that both additive and non-additive gene actions were involved in governing trait inheritance. The high GCA to SCA ratios calculated for all the studied traits indicate that additive genetic effect was predominant. Parental lines, Mwangaza, Lunyuki, Salama M-57, Salama M-19, IRAT 256 and Salama M-55, which had negative GCA effects for RYMVD, and families such as SARO × Salama M-55, IRAT 245 × Rangimbili, Rangimbili × Gigante and Rangimbili × Mwangaza, which had negative SCA effects for RYMVD were selected for RYMV resistance breeding. The crosses such as Rangimbili × Gigante, Gigante × Salama M-19 and Rangimbili × Salama M-55 were selected due to their desirable SCA effects for GY. The predominance of additive gene effects for agronomic traits and RYMVD resistance in the present breeding populations suggest that rice improvement could be achieved through gene introgression using a recurrent selection method. Overall, the present study resulted in selection of agronomically superior and RYMV resistant breeding parents and new rice families for further evaluation and variety release in Tanzania.