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Genetic Diversity and Population Structure Analysis of Asian and African Aromatic Rice (Oryza Sativa L.) Genotypes

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Genetic Diversity and Population Structure Analysis of Asian and African Aromatic Rice (Oryza Sativa L.) Genotypes Journal of Genetics (2019) 98:92 © Indian Academy of Sciences https://doi.org/10.1007/s12041-019-1131-0 RESEARCH ARTICLE Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes ANURAG MISHRA1,2, PUSHPENDRA KUMAR2∗, MD. SHAMIM3, KAPIL K. TIWARI4, PARVEEN FATIMA2, DEEPTI SRIVASTAVA5, RAJENDRA SINGH6 and PRASHANT YADAV7 1Division of Genetics, Indian Agricultural Research Institute, New Delhi 110 012, India 2Department of Agricultural Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110, India 3Department of Molecular Biology and Genetic Engineering, Dr.Kalam Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur 813 210, India 4Department of Plant Molecular Biology and Biotechnology, C. P. College of Agriculture, S. D. Agricultural University, S. K. Nagar 385 506, India 5Integral Institute of Agricultural Science and Technology, Integral University, Lucknow 226 026, India 6Zonal Research Station, Nagina, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut 250 110, India 7Directorate of Rapeseed Mustard Research, Bharatpur 321 304, India *For correspondence. E-mail: [email protected]. Received 18 October 2018; revised 2 April 2019; accepted 14 June 2019; published online 6 September 2019 Abstract. Rice germplasms collected from different regions could be used as valuable resources for the future breeding programme. For the utilization of such collections, knowledge about the level and distribution of genetic diversity among these collections will facilitate the breeder. In this study, we report the phenotypic correlation, biochemical quality parameters and population genetic analysis of 35 rice accessions including 34 aromatic rice from different countries and a nonaromatic, Nagina 22, a well-known drought resistance variety. Further biochemical quality analysis, gel consistency test, molecular diversity analysis with 55 simple sequence repeat markers, population structure analysis and pair wise FST analysis were also conducted to assess the genetic diversity. The collected rice genotypes showed significant variability in different agronomic traits, i.e. spikelet per panicle, branches per panicle etc. Results obtained from the above tests demonstrated the importance of regional genetic studies for understanding the diversification of aromatic rice in Asian and African rice. Keywords. basmati rice; aroma; alkali spreading value; gel consistency; amylose; diversity; simple sequence repeat primers. Introduction chemical compound 2-acetyl-1-pyrroline (2AP). Due to the presence of aroma in aromatic rice, they are in higher Rice (Oryza sativa L.) is one of the most widely demand than nonaromatic rice and also plays a vital role cultivated crops in the world. It is a diverse crop, due to in global rice trading (Blakeney et al. 1992; Weber et al. its adaptation to different geographical, ecological and 2000; Shobha et al. 2006). Aromatic rice can be further climatic regions. Most of the world’s rice is cultivated grouped into long and short grain type. Among the long and consumed in Asia, home for more than half of the grain aromatic rice, Basmati rice is more valuable because global population (Chakravarthi and Naravaneni 2006). of its cooking quality and are at higher demand. Basmati On the basis of aroma, rice can be grouped into aromatic rice elongates at least twice its original size after cook- and nonaromatic. Aromatic rice (scented rice or fragrance ing and has a delicious taste, superior aroma as well as rice) is very popular in Asia, United States, Europe and distinct flavour. India and Pakistan are the traditional in Middle East. Aroma in rice is due to the presence of producers and exporters of Basmati rice. In international 1 92 Page 2 of 19 Anurag Mishra et al. rice market, Basmati rice fetches three times higher price in cases where the morphological markers are inaccurate. than high-quality nonBasmati rice. Quality parameters Genetic diversity, relationship and population structure like grain dimensions, rice colour, texture of cooked rice, studies among the rice genotypes are valuable for different intensity of aroma and cooking quality analysis revealed purposes (Ndjiondjop et al. 2018). These purpose include large variation in rice under different agro-climatic con- the selection of parental combinations for the creation of ditions. Cooking quality traits of rice also varied despite different progenies that are phenotypically superior and having similar amylose content (AC), gel consistency (GC) with significantly higher yield potential compared to their and alkali spreading value (ASV). However, any aromatic parents (Mohammadi and Prasanna 2003). In the present rice is not accepted as Basmati in the trade (Sharma and study, we conducted morphological, biochemical, molec- Goel 2011). The molecular or DNA markers are preferred ular characterization along with diversity analysis of these over the traditional morphological and protein markers, aromatic and nonaromatic rice genotypes. The informa- because molecular markers are stable at different environ- tion generated in the present study can be further used in mental conditions as well as various developmental stages the aromatic rice breeding programme. (Yong-Jin et al. 2009). Among the molecular markers, sim- ple sequence repeat (SSR) is widely used in genetic diversity and gene pool study. SSR or microsatellite markers are tandem repeats of few nucleotides interspersed through- out the genome and can be amplified using primers that Materials and methods flank these regions (Grist et al. 1993). Various SSR mark- ers that varied in the degree of polymorphism have been Plant materials developed and their position is mapped in rice (Temnykh et al. (2000); McCouch et al. (2002)). Diversity assessment Thirty-five diverse rice germplasms collected from differ- of Indian rice germplasms have been conducted by the ent sources were sown in the randomized block design help of various researchers using molecular markers (Saini (RBD) manner with three replication at the field of the et al. 2004; Ram et al. 2007; Sundaram et al. 2008; Kumar Crop Research Centre and Laboratory, Sardar Vallab- et al. 2010; Sivaranjani et al. 2010; Vanniarajan et al. 2012). hbhai Patel University of Agriculture and Technology, Taxonomic classification using molecular marker is a nec- Meerut. Data of different parameters were recorded in two essary step to determine population structure especially consecutive years (figure 1; table 1). Figure 1. Different location of countries from where genotypes were taken for the study of diversity. Asian and African aromatic rice genotypes Page 3 of 19 92 Table 1. Detailed information of aromatic rice genotypes used in the study. No. of ancestor Release Genes for Genotype Pedigree used year Origin important traits 1 Basmati 370 Pure line selection for – 1962 Pakistan Traditional basmati export Dehradun traditional quality, long duration, LS basmati 2 PusaSugandh 4 P614-1-2/P 614-2-4-3 2005 India Evolved basmati irrigated, super fine, semidwarf, long duration, LS 3 Taraori basmati Pure line selection from 1996 Taroarikernal, Traditional basmati, Karnal local India semidwarf, long duration 4 Type 3 basmati Pure line selection for 1990 Dehradun, Traditional basmati, basmati Dehradun basmati India tall long duration, export quality, LS 5 Pusa basmati 1 Pusa 150/Karnal local 3 1996 India Evolved basmati high yield, irrigated, super fine, semidwarf, short duration, export quality, LS 6 Basmati 386 Pure line selection from – 1994 Punjab, India Traditional basmati export Karnal local quality, super fine and long duration, LS 7 PusaSugandh 5 Pusa 3A× Haryana India Medium duration irrigated, basmati super fine, semidwarf, LS 8 Vallabh basmati 22 Pusa 1121 × Type 3 2009 India Export quality, medium duration, super fine, LS 9 Vallabh basmati 21 Khalasa 7/Pusa 2013 SVPU&T, Evolved basmati 1121/Type-3 Meerut, India 10 Haryana basmati Sona/Basmati 370 7 1991 Pau, India Basmati 11 Basmati CSR 30 BR4-10/Basmati 370 – 2001, 2012 CSSRI, Evolved basmati, salinity KernaL tolerant. 12 Ranbir basmati Single plant selection 1996 Jammu Basmati &Kashmir, India 13 Vallabh basmati 24 Pusa 1121×Type 3 2015 SVPU&T, Export quality, medium Meerut, India duration, super fine, LS 14 Kalanamak Land race Sidharthnagar, Aromatic, short grain India 15 IR7734-93-2-3-2 NSIC RC 148/PSB RC 7 2002 IRRI Aromatic 18//NSIC RC 148 16 IR60080-46A IR47686-08-4-3/CT 12 1996 IRRI Aromatic 6516-21-4-4 17 IR78554-145-1-3-2 IR72861-13-2-1-2/IR- 14 IRRI Aromatic 68450-36-3-2-3 18 IR78006-55-2-3-3 IR67406-6-2-3/IR72860- 13 2005 IRRI Aromatic 80-3-3-3 19 IR77736-54-3-1-2 NSIC RC 148/PSB RC 7 2002 IRRI Aromatic 64//NSIC RC 148 20 IR77512-2-1-22 IR68726-3-3-1- 2002 IRRI Aromatic, semidwarf 2/IR71730-51-2 21 IR78537-32-1-2-1 IR65610-38-2-4-2-6- 14 2005 IRRI Aromatic 3/IR60912-93-3-2-3-3 22 WAB99-84 ITA 257/WABUKA 10 1995 Warda Aromatic 23 TOX3440-17-1-1-1-1-1 TOX891-212-1-201- 6 1998 Warda Aromatic, resistant to shield 105/TOX3056-5-1 bug 24 WAS515-B-10A-1-4 Unknown – 2000 Warda Aromatic 25 TOX3867-19-1-2-3-3 TOX3118-78-2-1/ITA 8 2000 Warda Aromatic 234 26 WAS272-B-B-5-H5 3290/WABC 165 6 2005 Warda Aromatic 92 Page 4 of 19 Anurag Mishra et al. Table 1 (contd) No. of ancestor Genes for Genotype Pedigree used Release year Origin important traits 27 TOX3226-5-2-2-2 ITA 235/ 8 1995 IITA Aromatic, resistant to IR9828-91-2-3/CT 19 blast and motile virus 28 WAS197-B-6-3-12 IR31851-96-2-3-2- 14 2005 Senegal Aromatic 1/IR66231-37-1-2 29 WAS197-B-5-2-5 IR31851-96-2-3-2- 14 2005 Senegal Aromatic 1/IR66231-37-1-2 30 WAS-197-B-5-2-16 IR31851-96-2-3-2- 14 2005 Senegal Aromatic 1/IR66231-37-1-2 31 WAS-197-B-4-1-25 IR31851-96-2-3-2- 14 2005 Senegal Aromatic 1/IR66231-37-1-2 32 WAS197-B-4-1-22 IR31851-96-2-3-2- 14 2005 Senegal Aromatic 1/IR66231-37-1-2 33 WAS197-B-6-3-16 IR31851-96-2-3-2- 14 2005 Senegal Aromatic 1/IR66231-37-1-2 34 WAS197-B-6-3-4 IR31851-96-2-3-2- 14 2005 Senegal Aromatic 1/IR66231-37-1-2 35 Nagina 22* – – Nagina, India Drought and heat stress resistance ◦ Evaluation of morphological traits 27–30 C.
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