Indian Journal of Biotechnology Vol 16, April 2017, pp 235-243 Genetic diversity assessment of pearl millet novel male sterile lines based on DNA polymorphism S K Singh*, V K Manga, Aravind Kumar Jukanti and Rakesh Pathak ICAR-Central Arid Zone Research Institute, Jodhpur 342 003, India Received 14 September 2015; revised 19 May 2016; accepted 7 June 2016 Lack of breakthrough in the yield is demanding drought tolerance and adaptation to the harsh arid environment by the released hybrids of pearl millet [Pennisetum glaucum (L.) R.Br.]. Fertility restoration patterns of F1 hybrids developed from crosses between male sterile (MS) lines possessing different cytoplasmic MS sources and a genetically diverse set of inbreds were exploited to circumvent this problem. In this paper, we report the extent of genetic diversity and relationship among 20 newly developed MS lines in P. glaucum using nuclear ribosomal DNA and RAPD polymorphism. High level of polymorphism (82.7%) among MS lines of P. glaucum by potential RAPD markers and with greater proportion of total genetic variation within population (87%) rather than among population (13%) revealed rich genetic diversity among the MS lines developed. Total gene diversity exhibited high levels of variability (HT=0.2337) and coefficient of gene differentiation (Gst=0.4651). Phylogram based on multiple sequences further delineated all the 20 MS lines with significant bootstrap values. SNPs at 16 places in ITS-1 are clear indication of phylogenetic utility of ITS-1 region, in particular, in developing bar code of pearl millet germplasm. The MS line CZMS-21 recorded with desirable traits like significantly higher grain yield and the maximum panicle harvest index was identified as a potential source of A4 cytoplasm for the development of stable single cross hybrid for arid environment. The genetic diversity among these MS lines with adaptation to arid environment shall be of significance in developing region specific hybrids. Keywords: nrDNA diversity, genetic diversity, male sterile lines, Pennisetum glaucum, RAPD Introduction Pearl millet [Pennisetum glaucum (L.) R.Br.] is the world’s most hardy, warm season, coarse cereal cultivated for grain, stover and green fodder mainly in arid and semi-arid regions of Africa and Asia 1 . India is the largest single producer of pearl millet occupying an area of 9. 3 M ha with a production of 8.3 M tones, contributing 42% of production in the world 2 . It is an important coarse cereal crop in western India and occupies about 38% of the total cereal crop area in the region. Mainly five states (Rajasthan, Maharashtra, Gujarat, Uttar Pradesh & Haryana) account for nearly 95% of the pearl millet cultivation area. With the advent of hybrids, the yield of pearl millet increased substantially in other states, while it was unsatisfactory in Rajasthan due to lack of desired adaptability and characteristics required for this region 3 . Under harsh conditions of arid zone, some landraces are also reported for out-yielding hybrids 4 . For successful cultivation of pearl millet hybrids in the arid western Rajasthan, it is important that the hybrids should be developed using parents that are adapted to the harsh climatic conditions of this region. Such hybrids would lead to better adaptation and performance, besides providing cultivar diversity, giving more choice to farmers. Hybrid vigour has been extensively utilized in pearl millet for increasing pearl millet productivity by utilizing male sterility for large scale production of hybrid seed. A high degree of heterosis in F1 hybrids, exceeding high yielding parental lines, up to 425%, have been realized 5 . Nevertheless, this increase in productivity has been primarily restricted to areas with assured rainfall or irrigation and fertilizers 6 . ICAR-Central Arid Zone Research Institute (CAZRI), Jodhpur, India has a strong restorer parent development programme 7,8 and is being utilized in crossing with male sterile (MS) lines from other sources like International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru (Telangana), India, to develop hybrids. Majority of the MS lines from other sources lacked adaptability to the harsh climatic conditions of arid region. Hence, a strong need was felt to develop pearl millet MS lines that are well adapted to this region leading to their —————— *Author for correspondence: sksingh1111@hotmail.com