Vol.:(0123456789) 1 3 Acta Physiologiae Plantarum (2019) 41:66 https://doi.org/10.1007/s11738-019-2855-4 ORIGINAL ARTICLE Transcriptomes of Indian barnyard millet and barnyardgrass reveal putative genes involved in drought adaptation and micronutrient accumulation Murukarthick Jayakodi 1  · Manimekalai Madheswaran 2  · Karthikeyan Adhimoolam 3  · Sampath Perumal 4  · Dhasarathan Manickam 3  · Thangaraj Kandasamy 2  · Tae‑Jin Yang 1  · Senthil Natesan 3,5 Received: 14 April 2018 / Revised: 28 March 2019 / Accepted: 1 April 2019 © Franciszek Górski Institute of Plant Physiology, Polish Academy of Sciences, Kraków 2019 Abstract Indian barnyard millet (Echinochloa frumentacea) is a rich source of dietary fiber, minerals and protein. The lack of genetic resources has slowed the discovery of genes involved in its nutrient accumulation and climate resilience. Here, we present the first transcriptomes of E. frumentacea [97,065 transcripts, including 65,276 protein-coding transcripts, over 90% of which have been functionally annotated, and 31,789 long noncoding RNA (lncRNA) transcripts] and its wild relative E. crus-galli (93,725 transcripts, including 68,480 protein-coding transcripts, 89% of which have been annotated). Comparative transcriptome analysis identified 4159 protein-coding and 2258 lncRNA transcripts in Indian barnyard millet that showed either up- or down-regulated expression when compared with E. crus-galli, and 3489 protein-coding transcripts unique to Indian barnyard millet were also detected. Additional analysis revealed that photosynthesis is likely crucial in the drought adaptation of Indian barnyard millet. We then identified possible genes regulation responsible for drought tolerance and Fe and Zn accumulation. Moreover, based on the simple sequence repeat (SSR)-containing sequence, 30 SSR primer pairs were arbitrarily selected, synthesized and used to screen the 30 E. frumentacea accessions. Of these, 10 SSR primers were polymorphic. Collectively, our results enhance the knowledge of micronutrient accumulation and drought tolerance in Indian barnyard millet, as well as of the genetic diversity of Echinochloa species. Keywords Drought · Simple sequence repeats · Indian barnyard millet · Micronutrients Introduction Barnyard millet (Echinochloa spp.) is the oldest domesti- cated millet and mainly growing in the semi-arid tropics of Asia and Africa. The genus Echinochloa belongs to Poaceae family and it includes 35 species (Mabberley 1997), includ- ing the major weed species of E. crus-galli (barnyard grass) Communicated by A.Chandra. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s11738-019-2855-4) contains supplementary material, which is available to authorized users. * Tae-Jin Yang tjyang@snu.ac.kr * Senthil Natesan senthil_natesan@tnau.ac.in 1 Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Republic of Korea 2 Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu 625104, India 3 Department of Biotechnology, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, Tamil Nadu 625104, India 4 Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada 5 Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu 641003, India