Genetic Diversity Of Aromatic Rice (Oryza Sativa L.) And Mapping Of The Fragrance Gene

Aromatic rice falls into the specialty category of cultivated rice. Aromatic rice isplaying a vital role in the international paddy rice trade market. Basmati rice is a type ofaromatic rice, grown mostly in India and Pakistan. It is renowned for its superfine grainqualities, distinct aroma and extra-elongation during cooking. South Asian countriesincluding India are the genetic diversity center of basmati rice. There is a fair aromaticrice germplasm in South Asian countries. It might be important for beneficialsupplement of aromatic rice and improvement of aromatic rice in our country tointroduce and make use of a series of aromatic rice genotypes from South Asiancountries. The objective of the present study was to reveal the molecular markers linkedto fragrance gene (fgr) and mapping of fgr, genetic diversity, population relationships,and core collection for breeding aromatic rice among aromatic rice genotypes fromSouth Asia and Guangxi of China, and non-aromatic native cultivars from Guangxi ofChina by using SSR primers. The main results of the study were presented as follows:1. A F₂ population, non-aromatic elite rice zhongdal4 as the female parent andaromatic rice UPRB45 from South Asia as male parent, was constructed by bulkedsegregant analysis (BSA). The fragrance of 220 single plants in F₂ population was tested.The ratio of 3: 1 for non-aromatic to aromatic plants indicated that a recessive nucleargene controlled the aromatic character in the aromatic rice UPRB45. Total 384 pairs ofSSR primers located on 12 chromosomes of rice genome were used for PCR to parentsand F₂ population. The results showed that two SSR markers RM223 and RM7356 onchromosome 8 were linked with the fragrant gene. The genetic distance of the two SSRmarkers to the fragrant gene was 5.3 cM and 11.0 cM, respectively.2. Nei's genetic distance of UPRH group (traditional aromatic rice from South Asia), B group (evolved aromatic rice from South Asia), and aromatic and non-aromatic nativecultivars from Guangxi of China was 0.78, 0.69, 0.59 and 0.58, respectively. Analysis ofNei's genetic distance showed that genetic diversity in South Asia traditional aromaticvarieties was significantly larger than that in the South Asia evolved aromatic varieties,while that in the evolved aromatic varieties from South Asia was significantly largerthan that in the aromatic varieties and non-aromatic native germplasm being planted inGuangxi. These study results indicated much rich genetic basis in the aromaticgermplasm from South Asia.3. Genetic diversity of 96 rice genotypes included 78 aromatic rice genotypes fromSouth Asia and 18 aromatic rice genotypes from Guangxi was assessed. A total of 85 and55 alleles were present in South Asia and Guangxi aromatic rice at the 16 SSR loci,respectively. The number of alleles per locus for respectic South Asia and Guangxiaromatic rice ranged from 3 to 13 and from 2 to 9 with an average of 5.31 and 3.44, andthe polymorphism information content (PIC) values ranged from 0.171 to 0.872 andfrom 0.099 to 0.765 with an average of 0.55 and 0.41, and the average geneticmultiplicity index (Hs) values ranged from 0.184 to 0.884 and from 0.105 to 0.792 withan average of 0.60 and 0.47, respectively. The results indicated the genetic diversity washigher in the aromatic rice germplasm from South Asia than that from Guangxi.4. The results of cluster analysis on the aromatic and non-aromatic rice genotypeswith 16 SSR markers showed the aromatic and non-aromatic varieties were basicallyclustered into two groups. Among the 78 aromatic varieties introduced from abroad, 57or 73.1% were clustered into a group, 18 or 23.1% clustered together with 14 Guangxiaromatic varieties, whereas only 3 or 3.8% clustered together with 24 Guangxi nativenon-aromatic varieties at the genetic distance 0.56. The cluster analysis indicated thatmost of the aromatic rice germplasm from South Asia or from Guangxi could beobviously confined to one cluster respectively. And the genetic and geographicaldifferences lied between the aromatic rice germplasm from South Asia and those fromGuangxi.5. The genetic diversity of six populations was evaluated by using 5 SSR markerslinked to fgr, which included the aromatic rice, non-aromatic indica and japonicapopulations from Guangxi, and UPRB, UPRH and B populations from South Asia aromatic rice genotypes. The highest genetic diversity for chromosome number 8 wasdetected among the B population. The genetic relationships among the 6 populationswere obtained by POPGENE analysis based Nei's genetic distance. The 6 populationswere clustered into two groups. Group I comprised the aromatic rice, non-aromaticindica and japonica populations from Guangxi. Groupâ…¡included UPRB, UPRH and Bpopulations from South Asia aromatic rice genotypes. This suggested that the geneticdifference lied between the aromatic rice genotypes from South Asia and that fromGuangxi. The genetic relationships among the 6 populations indicated that the aromaticrice genotypes from South Asia had developed a special aromatic rice type.6. Based on Nei-Li similarity coefficients matrix, japonica-india type andgeographical resource of original collection, the preliminary core collection for breedingaromatic rice, comprised of twenty-four rice genotypes, was constructed after four-timeclusters. The average number of alleles per locus, effective number of alleles per locus,total index of gene diversity, average index of gene diversity and coefficient of genedifferentiation is 5.25, 3.265, 0.8656, 0.6509 and 0.2478, respectively, in the corecollection; while 6.25, 3.348, 0.8883, 0.6525 and 0.2659, respectively, in original collection.The results indicated the genetic diversity between the core collection and the originalcollection was very similar, and the established core collection could represent thegenetic diversity of the original collection. It could be applied in breeding aromatic rice.