Genetic Diversity Studies on Selected Rice (Oryza sativa L.) Genotypes based on Gel Consistency and Alkali Digestion

¹Department of Biochemistry and Biotechnology, Kenyatta University, Nairobi, Kenya

²Molecular Laboratory, Kenya Bureau of Standards, Kenya

Corresponding Author:

Lagat Rose Chemutai
Department of Biochemistry and Biotechnology, Kenyatta University, P.O. Box 43844-00100, Nairobi, Kenya
Tel: +254712848915
E-mail: roselagat76@gmail.com

Received Date: May 26, 2016; Accepted Date: August 01, 2016; Published Date: August 09, 2016

Citation: Chemutai LR, Musyoki MA, Kioko WF, Mwenda NS, Muriira KG, et al. (2016) Genetic Diversity Studies on Selected Rice (Oryza sativa L.) Genotypes based on Gel Consistency and Alkali Digestion. J Rice Res 4:172. doi: 10.4172/2375-4338.1000172

Copyright: © 2016 Chemutai LR, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Abstract

Knowledge of rice genetic diversity is necessary to ascertain the germplasm conservation and the development of improved rice genotypes with good quality traits through various breeding programs. The aim of this study was to determine the genetic diversity based on gel consistency and alkali digestion among selected Kenyan and Tanzanian genotypes using SSR markers. PowerMarker version 3.25, GenAlEx version 6.41 and DARwin 6.0.12 statistical software were used to carry out data analysis. The number of alleles per locus ranged from 2 to 4 with an average of 2.75 across the 8 markers used. Polymorphic information content (PIC) ranged from 0.5224 (RM577) to 0.1411 (RM85) with an average of 0.3673 observed across all the markers. Gene diversity ranged from 0.5764 (RM577) to 0.1528 (RM85) with an average of 0.4181 with one rare allele was detected at RM577 loci. Pairwise genetic dissimilarity matrix ranged from ranged from 0.9333 to 0.1818 with the least genetic distance being observed between IR 54 and BS 370 while the highest, 0.9333 being between Saro 5 and IR 2793. The unweighted neighbour joining tree clustered the rice genotypes into three major clusters and subsequent sub clusters hence effectively differentiating the Kenyan and Tanzanian genotypes based on gel consistency and alkali digestion. This clustering was complemented with the findings in the principal coordinate analysis. These results show that determination of genetic diversity using SSR markers cam be successfully achieved. In this study RM577 was the best and most informative SSR marker given it showed the highest PIC, gene diversity and allele per locus. In addition, it’s the only marker that showed a rare allele at 400 bp.

Keywords

Evaluation; Heat tolerance; Flowering stage; Rice (Oryza Sativa L.)

Introduction

High temperature is a problem in rice production throughout the tropical areas of Asia. If it exceeds the critical temperature which affects the normal physiological activities of rice in different growth stages. As a result growth stunts, pollen sterility and low spikelet fertility occurs, yield reduces drastically. Global warming has become one of the most complicated problems affecting agricultural productivity. It was reported that global emissions of carbon dioxide caused by human activities reached a record high in 2011 and will likely increase in succeeding years, thus contributing to the global increase in temperature [1,2]. Global climate model projections summarized in the 2007 Fourth Assessment Report (AR4) by the Intergovernmental Panel on Climate Change (IPCC) indicated that, during the 21st century, global surface temperature is likely to further rise by 1.1 to 2.9°C for their lowest emissions scenarios and by 2.4 to 6.4°C for their highest emissions scenarios [3]. The increase in temperature has been striking and can cause irreversible damage to plant growth and development [4]. It has been shown a 7-8% rice yield reduction for each 1°C increase in daytime temperature from 28°C to 34°C [5]. Rice has been cultivated under a wide range of climatic conditions. Almost 90% of the world’s rice is grown and consumed in Asia, where 50% of the population depends on rice for food. However, the rice crop during the sensitive flowering and early grain-filling stages is currently exposed to temperatures higher than the critical threshold of 33°C in South Asia (Bangladesh, India) and Southeast Asia (Myanmar, Thailand) [6]. Though there has been no systematic monitoring and evaluation of temperature stress-induced yield losses worldwide, regional high temperature damages were observed in many tropical and subtropical countries, such as Pakistan, India, Bangladesh, China, Thailand, Sudan, and some other African countries [7,8]. Hence, heat stress poses a serious threat to sustaining rice production in the most productive regions of tropical Asia. Thus, heat tolerance has to be integrated into future rice breeding programs. Cultivated rice is more tolerant to high temperature than many other major food crops, such as maize, wheat and potato, but many rice varieties are still sensitive to high temperature at reproductive stages. Wide genetic variability exists in the current genetic resources for resistance to heat stress [9,10]. This potential could be explored to screen rice germplasm with heat tolerance for developing current well-adapted varieties for future warmer climates. Screening for heat-tolerant varieties has been done in some Asian countries. Mackill et al. [11] compared the hightemperature tolerance in tolerant and susceptible cultivars of rice and observed a marked decrease in the number of pollen shed on the stigma in susceptible lines, which led to reduced spikelet fertility. N22, an Indian aus variety, has been identified as one of the most heattolerant accessions [12] and it has been used as a check variety for many studies on heat tolerance. Environmental temperature extremes coinciding with the critical stage of plant development often threaten crop productivity. In general, the reproductive stage is more sensitive than the vegetative stage in many crop species [13]. In rice development, almost all growth stages are affected by high temperature. However, high temperature is more injurious if it occurs just before or during anthesis [14]. The two most sensitive stages are flowering (anthesis and fertilization) and booting (microsporogenesis). Exposure at anthesis even for less than an hour at 33.7°C may result in spikelet sterility [15], which will greatly increase at temperature above 35°C [16]. To facilitate breeding for heat tolerant varieties, Experiments were therefore carried out under different temperature resumes in field conditions: (i) to evaluate the effect of high temperature during anthesis on the morphology of the reproductive organs and to identify heat-sensitive physiological processes; (ii) to identify and compare high-temperature-responsive anther proteins in rice genotypes at anthesis; and (iii) to determine genotypic differences in reproductive organ morphology, and physiological processes to spikelet fertility of rice. For this reason we need such varieties which can tolerate high temperature without any abnormality. IRRI has been working about the problem and developed much more lines to face the unwanted situation. Out of this, 1217 entries are evaluated at BRRI to observe their performance. Critical sterility point 15-20 days before heading.

Materials and Methods

An experiment was established at different transplanting date (40 days old seedlings) to find critical sterility point of a specific variety during late boro season to capture high temperature (>32°C). At flowering time and to find the effects of different temperature regimes on the rate of spikelet sterility and grain filling. The experiment was set-up following split-plot design. Fertilizers were applied @ 270:130:120:70:10 kg/ha urea, triple super phosphate (TSP), muriate of potash (MP), gypsum and zinc sulphate respectively. Urea was top dressed with three equal splits at 15-20 days and 35-40 days after transplanting and at booting stage. Remaining fertilizers TSP, MP, gypsum and zinc sulphate were applied at the time of final land preparation. Intercultural operations, insecticide spraying and other activities were done when necessary. Data were collected for specific objectives when required. Temperature data will be recorded. Best transplanting time that matched with high temperature period of Bangladesh will be detected. Critical sterility point of a specific variety during late boro season will be identified (Selection Criteria).

Statistical analyses

Data collected on different parameters under study were statistically analyzed to ascertain the significance of the experimental results using the Statistix 10 computer package program.

Results and Discussion

Genetic diversity for heat tolerance is important for breeding new varieties for areas affected by high temperatures during the ricegrowing season. Some heat-tolerant varieties have been identified in previous studies [14,16-18]. In our study, we screened 1217 lines from different hot rice growing regions; however, very few varieties (about 2%) showed some degree of heat tolerance. The identified donors of heat tolerance can be used for improving the heat tolerance of future rice varieties and for genetic studies to understand the mechanism of heat tolerance. However, most of the heat-tolerant varieties are traditional varieties with undesirable agronomic characters, which make it difficult to use them in breeding directly. These varieties could be widely used as donors of heat tolerance in our breeding programs. Data were analyzed and best heat tolerant materials were selected based on high grain filling under high temperature (average 32°C at flowering stage). 1217 entries were evaluated in field condition at Gazipur, Bangladesh under high temperature during March to July (Late boro season). During the panicle initiation period of all materials, maximum temperature was in May and June (around 35°C). In July temperature was reduced slightly. As what Yoshida et al. [15] discussed about heat tolerance at the flowering stage, we reconfirmed that temperature of 37-38°C could be used for phenotyping most of the rice populations for genetic studies, and 38-39°C could be used for screening the most heat-tolerant genetic resources from a gene bank collection and breeding populations [19]. But, for heat tolerance at the booting stage, the treatment should be at least 1°C higher than that for the flowering stage. Out of them - twenty (20) entries were selected on the basis of their high yield, high spikelet fertility% and other agronomic traits under high temperature at panicle initiation to flowering period. It was reported that the rice plant is most sensitive to high temperature at heading (flowering) time and second most sensitive at about 9 days before heading (booting), and high temperature before anthesis has less effect on spikelet fertility [14]. Yield level and spikelet fertility% of these selected entries were ranged from 11.92 to 20.02 gm/plant and 61% to 86% (Table 1). Most of the entries have short or medium growth duration (120-138 days) with medium yield level. Plant height of most of entries was short - below 100 cm. Disease and insect reaction are low. The highest yield was found in IR 86991-146-2-1-1 (20.02 gm/plant.) followed by IR 87606-109-2-2 (19.35 gm/plant). Highest spikelet fertility% was observed in IR 88268-107-1-1 (86%) followed by IR 88268-124-2-3 (84%). Two entries (IR 87606-109-2-2 and IR 86991-146-2-1-1) are selected as heat tolerance for further evaluation and crossing program. From the poor performed entries two were selected as low yielding control (IR 86960-66-1-2-1 and IR 86977-134-1-1-1) due to their low yield and low spikelet fertility (Figure 1) (Tables 2 and 3).

Table 1: Yield and Ancillary Characters of Selected materials from 1217 entries.

Figure 1: IRRI heat tolerant materials at BRRI, Gazipur

Table 2: Selected Entries for Poor Performance

Table 3: Temperature Record during Panicle Initiation stage to Flowering

Conclusion

Selected 20 entries could be evaluated in different seasons for their heat tolerance and high yield performance and could be used in different crossing program. IR 87606-109-2-2 and IR 86991-146-2-1-1 were found as tolerate to heat during flowering. These two entries are using in crossing program to develop heat tolerant varieties with high yield.

References

1. Maraseni TN, Mushtaq S, Maroulis J (2009) Greenhouse gas emissions from rice farming inputs: a cross-country assessment. J AgricSci 147: 117-126.
2. Smith P, Olesen JE (2010) Synergies between the mitigation of and adaptation to climate change in agriculture. J AgricSci 148: 543-552.
3. Meehl GA, Stocker TF, Collins WD, Friedlingstein P, Gaye AT, et al. (2007) Global limate Projections. In: Solomon S, Qin D, Manning M, Chen Z, Marquis M, et al. (ed.) Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA.
4. Wahid A, Gelani S, Ashraf M, Foolad MR (2007) Heat tolerance in plants: an overview. Environ. Exp Bot 61: 199-233.
5. Baker JT, Allen Jr LH, Boote KJ (1992) Temperature effects on rice at elevated CO2 concentration. J Exp Bot 43: 959-964.
6. Wassmann R, Jagadish SVK, Sumfleth K, Pathak H, Howell G, et al. (2009) Regional vulnerability of climate change impacts on Asian rice production and scope for adaptation. AdvAgron 102: 93-105.
7. Matsushima S, Ikewada H, Maeda A, Honda S, Niki H (1982) Studies on rice cultivation in the tropics. In: Yielding and ripening responses of the rice plant to the extremely hot and dry climate in Sudan. Jpn J Trop Agric 26: 19-25.
8. Osada A, Sasiprapa V, Rahong M, Dhammanuvong S, Chakrabandho H (1973) Abnormal occurrence of empty grains of indica rice plants in the dry hot season in Thailand. Proc Crop SciSocJpn 42: 103-109.
9. Prasad PVV, Boote KJ, Allen Jr. LH, Sheehy JE, Thomas JMG (2006) Species, ecotype and cultivar differences in spikelet fertility and harvest index of rice in response to high temperature stress. Field Crops Res 95: 398-411.
10. Matsui T, Omasa K (2002) Rice (Oryzasativa L.) cultivars tolerant to high temperature at flowering: anther characteristics. Ann Bot 89: 683-687.
11. Mackill DJ, Coffman WR, Rutger JN (1982) Pollen shedding and combining ability for high temperature tolerance in rice. Crop Sci 22: 730-733.
12. Jagadish S, Muthurajan R, Oane R, Wheeler T, Heuer S, et al. (2010) Physiological and proteomic approaches to address heat tolerance during anthesis in rice. J Exp Bot 61: 143-156.
13. Hall AE (1992) Breeding for heat tolerance. Plant Breed. 10: 129-168.
14. Satake T, Yoshida S (1978) High temperature induced sterility in indica rice at flowering. Jpn J Crop Sci 47: 6-17.
15. Yoshida S, Satake T, Mackill DJ (1981) High temperature stress in rice (review). IRRI Res Paper Series 67: 5.
16. Matsui T, Omasa K, Horie T (1997) High temperature induced spikelet sterility of japonica rice at flowering in relation to air humidity and wind velocity conditions. Jpn J Crop Sci 66: 449-455.
17. Matsui T, Omasa K, Horie T (2001) The differences in sterility due to high temperatures during the flowering period among japonica rice varieties. Plant Production Science 4: 90-93.
18. Jagadish S, Crauford PQ, Wheeler TR (2008) Phenotyping parents of mapping populations of rice (Oryzasativa L.) for heat tolerance during anthesis. Crop Sci 48: 1140-1146.
19. Ye C, Argayoso M, Redoña E, Sierra S, Laza M, et al. (2012) Mapping QTL for heat tolerance at flowering stage in rice using SNP markers. Plant Breed 131: 33-41.