SSR Markers Based Genetic Diversity in Nepalese Maize Landraces

SAARC J. Agric., 18(1): 23-37 (2020) DOI: https://doi.org/10.3329/sja.v18i1.48379 Research Article SSR MARKERS BASED GENETIC DIVERSITY IN NEPALESE MAIZE LANDRACES B.K. Joshi1*, J. Rawat2, B. Adhikari1 and R. Pokhrel1 1 National Agriculture Genetic Resources Center, NARC; Khumaltar, Kathmandu, Nepal; 2 Himalayan College of Agricultural Sciences & Technology (HICAST), Kalanki Kathmandu, Nepal ABSTRACT Knowledge on genetic diversity is necessary for developing new varieties and managing diversity for future use. Five SSR markers were used to develop the DNA finger prints and to assess the diversity of 23 Nepalese maize landraces. Five locus-based DNA finger prints have distinguished majority of the landraces. The average number of alleles was 2 per locus. Umc1333 marker had shown the highest gene diversity, heterozygosity and polymorphism information content (PIC). At landrace level, the highest gene diversity, heterozygosity and PIC values were found in Seto Local and Seti Makai-3. 23 maize landraces formed four clusters and these clusters were related with seed color. Name of landraces also reflected genetic similarity. Genetically similar landraces can be pooled for conservation and creating dynamic diversity rich population. Distantly related landraces (Bhirkaule, Local Seto Makai, Seto Makai-1, Makai Makai-1761) can be used in breeding program. Detection of low genetic diversity might be due to bottleneck effects during the collection of these landraces from farmers. Therefore, collection strategy needs to be revised for capturing maximum diversity. Keywords: Gel analysis, Gene diversity, Maize landrace, SSR marker, DNA finger print INTRODUCTION Maize is the second most important staple food crop in Nepal and is grown under a wide range of agro-climatic and ecological conditions both in hill and plain areas under rainfed complex farming system. The development of high yielding varieties and populations of maize always remains in the target of many countries. Exploration and collection of diversity at genetic levels are the prerequisites for maize breeding. Nepal, being climatically and socioeconomically diverse, possesses a large number of * Corresponding author: Received: 19.04.2020 Accepted: 20.06.2020 Joshi et al. 24 different maize landraces adapted from low altitude i.e. 60 AMSL to more than 3000 AMSL (Upadhyay et al., 2003; Joshi et al., 2017; NAGRC, 2019). But they are not given due emphasis on research and education (Joshi et al., 2020), and therefore many of them are at risk of loss from the field. This situation also demands the generation of knowledge on diversity to manage diversity both on-farm and in-situ. Diversity can be measured from the ecosystem to allelic levels using different approaches and markers. DNA based markers are found very reliable and are playing a significant role in maize breeding. Among the DNA markers, SSR marker is robust, co-dominant, hypervariable, abundant, and uniformly dispersed in plant genomes (Powell et al., 1996; Mohan et al., 1997; Senior et al., 1998). These markers have been extensively used for genetic diversity analysis, parental lines selection, heterosis, and combining ability studies in maize (George et al., 2004; Nguyen et al., 2012). In an analysis of 45 maize inbreeds involving a set of 22 primer pairs derived from maize genome and 20 primer pairs derived from rice genome generated 132 and 181 markers with an average polymorphism information content (PIC) value of 0.83 and 0.38, respectively (Ranatunga et al., 2009). Clustering pattern of these genotypes based on SSR marker profiles were different from that of morphometric traits (Ranatunga et al., 2009). Among the four important maize varieties in Nepal, 30 SSR markers revealed an average heterozygosity of 45.07% for varieties, ranging from 35.23% in Rampur Composite to 54.64% in Khumal Yellow variety (Gurung et al., 2010). Molecular marker-assisted breeding is contributing significantly to increase the grain yield of maize in USA (Prasanna et al., 2010) but, conventional breeding predominant the maize breeding in Nepal. So far 93 varieties of maize have been released and registered and 520 accessions are being conserved in National Genebank (NAGRC, 2019) but not fully utilized in breeding program (Joshi, 2017). These collections in the Genebank could be valuable resources for advancing the maize breeding for which genetic level information is necessary to generate. Knowledge of genetic variation and relationships among landraces is important to understand the genetic variability available, to estimate the rare genotypes and alleles, to adopt suitable conservation strategies, to select suitable landraces for developing hybrid as well as high yielding maize populations. Molecular markers greatly facilitate for understanding genetics of a large number of collections conserved in the Genebank. This research was, therefore, conducted to generate DNA profiles of maize landraces, to assess the genetic diversity, to relate maize landraces (accessions) in terms of their genetic information using SSR markers. MATERIALS AND METHODS Maize landraces A total of 23 maize landraces from National Genebank, Kathmandu were used in this study. Their passport details are given in Table 1. These were collected from 11 25 GENETIC DIVERSITY IN NEPALESE MAIZE LANDRACES districts (Ramechhap, Dadeldhura, Dailekh, Pyuthan, Kaski, Dolpa, Bajura, Lalitpur, Nuwakot, Rasuwa and Bhojpur) within an altitudinal range from 60 to 2530 AMSL. These landraces were collected before 2000 and regenerated latter in Khumaltar. Table 1. Details of maize landraces used in this study Latitude (D) Longitude (D) Altitude (m) 27.596 86.264 1783 Khadga Bahadur Karki 2012 NK NK NK NK NK Amargadi-2, Dadeldhura NK NK 1835 NK 2008 11044 Radimadi, Dailekh NK NK 800 NK 2008 Seto Local 11054 Dhalea, Pyuthan NK NK 800 NK 2008 Makai 11066 Rimal-7, Kaski NK NK 1200 NK 2008 7 Seto Makai-1 C0691 Likhu-4 Likhu, Dolpa NK NK 2530 NainaPahadi 2011 8 Ratomakai NPGR-01706 Bortan, Bajura NK NK 1720 NK 1985 9 Pahenlo makai-1 C5109 Dalchoki-3, Goth Bhanjyang, Lalitpur NK NK 1900 Krishna Sanjel 2014 10 Mailisathiyama kai C5051 Ratamate-1, Raigaun, Nuwakot 27.8575 85.0625 1387 Shiva Kumari Rai 2013 11 Amrikane Makai C4937 Kaule-6, Nuwakot 28.0928 85.2531 1509 Santa Lama 2013 12 Bhirkaule C5046 Dhaibung-6 Dhaibung, Rasuwa 27.9997 85.2089 1563 ChitraKumariNeup ane 2013 13 Sathiyamakai C5050 Ratamate-1, Raigaun, Nuwakot 27.8575 85.0625 1387 Shiva Kumari Rai 2013 14 Local Seti Makai C5169 Gupteshwor-8, Bhojpur NK NK 60 Meghraj Shrestha 2014 15 Dharim Choti Paheli C5170 Ranibash-4, Bhojpur NK NK 6o Mitra Maya Rai 2014 16 Paheli Makai-2 C5172 Champe-5, Bhojpur NK NK 60 Chhatra Rana Magar 2014 17 Paheli Makai-3 C5174 Pancha-2, Bhojpur NK NK NK Bahadur Rai 2014 18 Sadiya Makai C5175 (...truncated)