News Update on Rice Genetics : Dec 2020

Microsatellite marker development, mapping and applications in rice genetics and breeding

Microsatellites are simple, tandemly repeated di- to tetra-nucleotide sequence motifs flanked by unique sequences. They are valuable as genetic markers because they are co-dominant, detect high levels of allelic diversity, and are easily and economically assayed by the polymerase chain reaction (PCR). Results from screening a rice genomic library suggest that there are an estimated 5700–10 000 microsatellites in rice, with the relative frequency of different repeats decreasing with increasing size of the motif. A map consisting of 120 microsatellite markers demonstrates that they are well distributed throughout the 12 chromosomes of rice. Five multiple copy primer sequences have been identified that could be mapped to independent chromosomal locations. The current level of genome coverage provided by these simple sequence length polymorphisms (SSLPs) in rice is sufficient to be useful for genotype identification, gene and quantitative trait locus (QTL) analysis, screening of large insert libraries, and marker-assisted selection in breeding. Studies of allelic diversity have documented up to 25 alleles at a single locus in cultivated rice germplasm and provide evidence that amplification in wild relatives of Oryza sativa is generally reliable. The availability of increasing numbers of mapped SSLP markers can be expected to complement existing RFLP and AFLP maps, increasing the power and resolution of genome analysis in rice. [1]

Hybrid rice: genetics, breeding, and seed production.

The subject is reviewed under the following headings: introduction, including China’s achievements, hybrid rice technology outside China, and bottlenecks and potential solutions; heterosis in rice, including concept of heterosis, performance of heterosis, genetic basis of heterosis, prediction of heterosis and approaches for utilization of heterosis; male sterility in rice, including morphology, cytology and histology of male sterile lines, physiological and biochemical basis, and genetic basis; breeding for three-line system hybrid rice, including breeding procedure, development of A and B lines, development of R lines, development of elite hybrid combinations, breeding for rice hybrids with resistance to insect pests and diseases, and breeding for rice hybrids with high grain quality; breeding for two-line system hybrid rice, including considerations, development of T(P)GMS lines, China’s progress and breeding for two-line system rice hybrids using chemical emasculators; wide compatibility and utilization of intersubspecific heterosis, including classification in rice, phenomenon of wide compatibility, genetics of wide compatibility traits, development of WCVs and utilization of intersubspecific heterosis; hybrid rice seed production, including China’s success, key techniques, specifics for CMS line multiplication and purification of parental lines; and future prospects, including breeding of diverse parental lines, molecular breeding, apomixis breeding, hybrid seed production and socioeconomic impact. [2]


Salt tolerance studies were conducted under controlled conditions by using solution and pot culture techniques at the International Rice Research Institute. Varieties Nona Bokra and Pokkali (tolerant), Damodar and Jhona 349 (moderately tolerant), and IR28 and IR35657-33-2 (sensitive) were selected for genetic analysis of traits under salinization (EC 12 dS/m) at the seedling and reproductive stages. Both additive and dominance effects were important in the inheritance of all the traits studied. Shoot length, Na and Ca content in the shoots, and dry weight of shoots and roots showed significant additive effects with a high degree of heritability. Genes controlling Na and Ca levels in shoots were found to be partially dominant. At least three groups of genes were found to be involved in the inheritance of Na and Ca levels at the seedling stage. Highly significant additive effects were also observed for plant height and yield/plant, with high heritability values. Selection on the basis of shoot length, Na level in the shoots, dry weight of shoots and roots, plant height, and yield/plant showing predominance of additive effects and high heritability values could lead to the development of salt-tolerant cultivars. [3]

Assessment of Genetic Variability and Correlation Coefficient to Improve Some Agronomic Traits in Rice

This study was conducted to evaluate genetic components, heritability and correlation coefficient effects of the parents and their F1 for some agronomic as well as yield and yield traits. A line x tester cross was conducted among the ten parents (four lines and six testers) in 2010 to produce (24) F1 crosses evaluated during 2011. The results indicated that both GCA showed highly significant for all studied traits. The mean squares of lines x testers interaction (SCA) exhibited highly significant differences for all studied traits. Higher estimates for non-additive or dominance genetic variance was computed for number of panicles / plant, number of filled grains / panicle and grain yield / plant in comparison with its corresponding evaluates of additive genetic variance. Concerning to heritability estimates, high values were observed in broad sense heritability. Meanwhile, evaluate of narrow-sense heritability were low to moderate for number of panicles / plant, number of filled grains / panicle, 1000-grain weight and grain yield / plant. Heritability estimates in narrow sense were relatively low for panicle weight and spikelet fertility percentage. As for correlation for grain yield / plant the results recorded highly positive correlation coefficient with each number of days to heading, plant height, number of panicles / plant, panicle length, panicle weight, fertility percentage and 1000-grain weight. [4]

Genetic Improvement of Rice in Nigeria for Enhanced Yeild and Grain Quality – A Review

The development of rice with high yield and grain quality is one of the main goals of rice breeding programs all over the world. In Nigeria, Rice breeders have been successful in improving the crop for different characteristics, tolerance to biotic and abiotic stresses. An example of rice variety developed for early maturity, high grain yield and quality is FARO 44(Sipi-692033), for tolerance to iron toxicity is FARO 52(WITA 4), for tolerance to African Rice Gall Midge is UPIA 2 (IWA 2) amongst others. A number of breeding methods such as Conventional Hybridization, Recurrent Selection, and Mutation breeding and Varietal Introduction from other countries can be used to create variability in rice to make improvement possible. Different research institutes in Nigeria, in collaboration with international NGOs have been intensifying efforts to improve the crop for different characteristics particularly for grain quality and high yield, adaptable to the country’s varying ecology. The development and introduction of tools of biotechnology into plant breeding have enhanced the breeding capacity of breeders, but these tools have not been fully integrated into rice breeding programs in the country. This paper highlights different breeding methods that can be used to develop new rice varieties, modify or improve already existing ones. Recommendations are also given in the direction of future research for enhancement of rice in Nigeria. [5]


[1] McCouch, S.R., Chen, X., Panaud, O., Temnykh, S., Xu, Y., Cho, Y.G., Huang, N., Ishii, T. and Blair, M., 1997. Microsatellite marker development, mapping and applications in rice genetics and breeding. In Oryza: From Molecule to Plant (pp. 89-99). Springer, Dordrecht.

[2] Li, J. and Yuan, L., 2000. Hybrid rice: genetics, breeding, and seed production. Plant breeding reviews, 17, pp.15-158.

[3] Akbar, M., Khush, G.S. and Hillerislambers, D., 1986. Genetics of salt tolerance in rice. In Rice Genetics I: (In 2 Parts) (pp. 399-409).

[4] Hefena, A., Sultan, M., Abdel-Moneam, M., Hammoud, S., Barutçular, C. and EL-Sabagh, A. (2016) “Assessment of Genetic Variability and Correlation Coefficient to Improve Some Agronomic Traits in Rice”, Journal of Experimental Agriculture International, 14(5), pp. 1-8. doi: 10.9734/JEAI/2016/29743.

[5] Babatunde Oluwaseyi, A., Nehemmiah, D. and Bolaji Zuluqurineen, S. (2016) “Genetic Improvement of Rice in Nigeria for Enhanced Yeild and Grain Quality – A Review”, Asian Research Journal of Agriculture, 1(3), pp. 1-18. doi: 10.9734/ARJA/2016/28675.

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