Vignesh Palanisamy, Mahadevaiah Channappa, Selvamuthu Kannan, Mahadeva Swamy Huskur Kumaraswamy, Sreenivasa Venkatarayappa, Appunu Chinnaswamy
Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641007 India.
ICAR-Indian Institute of Horticultural Research, Hesaraghatta Lake Post, Bangalore, 560089 India.
3 Biotech. 2024 Jan;14(1):24. doi: 10.1007/s13205-023-03867-7. Epub 2023 Dec 29.
Soil salinity and saline irrigation water are major constraints in sugarcane affecting the production of cane and sugar yield. To understand the salinity induced responses and to identify novel genomic resources, integrated de novo transcriptome and small RNA sequencing in sugarcane wild relative, salt tolerant accession IND 99-907 and salt-sensitive sugarcane genotype Co 97010 were performed. A total of 362 known miRNAs belonging to 62 families and 353 miRNAs belonging to 63 families were abundant in IND 99-907 and Co 97010 respectively. The miRNA families such as miR156, miR160, miR166, miR167, miR169, miR171, miR395, miR399, miR437 and miR5568 were the most abundant with more than ten members in both genotypes. The differential expression analysis of miRNA reveals that 221 known miRNAs belonging to 48 families and 130 known miRNAs belonging to 42 families were differentially expressed in IND 99-907 and Co 97010 respectively. A total of 12,693 and 7982 miRNA targets against the monoploid mosaic genome and a total of 15,031 and 12,152 miRNA targets against the de novo transcriptome were identified for differentially expressed known miRNAs of IND 99-907 and Co 97010 respectively. The gene ontology (GO) enrichment analysis of the miRNA targets revealed that 24, 12 and 14 enriched GO terms (FDR < 0.05) for biological process, molecular function and cellular component respectively. These miRNAs have many targets that associated in regulation of biotic and abiotic stresses. Thus, the genomic resources generated through this study are useful for sugarcane crop improvement through biotechnological and advanced breeding approaches.
The online version contains supplementary material available at 10.1007/s13205-023-03867-7.
土壤盐分和含盐灌溉水是甘蔗生产的主要限制因素，影响甘蔗产量和糖分产量。为了解盐分诱导的响应并鉴定新的基因组资源，对甘蔗野生近缘种、耐盐品种IND 99 - 907和盐敏感甘蔗基因型Co 97010进行了从头转录组和小RNA测序整合分析。分别在IND 99 - 907和Co 97010中发现了62个家族的362个已知miRNA和63个家族的353个miRNA含量丰富。miR156、miR160、miR166、miR167、miR169、miR171、miR395、miR399、miR437和miR5568等miRNA家族最为丰富，在两种基因型中均有十多个成员。miRNA的差异表达分析表明，分别在IND 99 - 907和Co 97010中有48个家族的221个已知miRNA和42个家族的130个已知miRNA差异表达。分别为IND 99 - 907和Co 97010差异表达的已知miRNA鉴定出针对单倍体镶嵌基因组的12693个和7982个miRNA靶标，以及针对从头转录组的15031个和12152个miRNA靶标。miRNA靶标的基因本体（GO）富集分析显示，分别有24、12和14个富集的GO术语（FDR < 0.05）与生物过程、分子功能和细胞成分相关。这些miRNA有许多参与生物和非生物胁迫调控的靶标。因此，本研究产生的基因组资源对于通过生物技术和先进育种方法改良甘蔗作物很有用。
在线版本包含可在10.1007/s13205 - 023 - 03867 - 7获取的补充材料。
