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One thousand and ninety four recombinant inbred lines derived from BPT-5204 × HP-14 cross were evaluated for sheath rot disease incidence under field conditions under aerobic and wetland transplanted situation. The population exhibited significant genetic variability among the RIL’s in both systems of rice cultivation. Response of the disease in both conditions was non-significant indicating that influence of planting system did not make any significant difference for this disease. Transgressive segregants were observed for yield attributing traits but not for sheath rot resistance. RILs HPR-1270, HPR-1416, HPR-212, HPR-260, HPR-1506, HPR-1407, HPR-1380 and HPR-312 in aerobic system and HPR-285, HPR-2129, HPR-978, HPR-702, HPR-94-2, and HPR-1514 in wetland system were found superior for both grain yield and sheath rot resistance. These genotypes could be evaluated further in large scale field trials for developing resistance varieties with superior grain yield.

Saccharum spontaneum L. is a perennial grass representing the most genetically diversified species in Saccharum genus. It has the potential to withstand severe biotic/abiotic stresses and frequently used as donor of stress tolerant genes in sugarcane improvement program through gene introgression. In this study, the phenotypic variation and molecular diversity of forty nine S. spontaneum accessions collected from Lohit and Changlang regions of Arunachal Pradesh, North Eastern India were investigated for morphometric traits and polymorphic STMS marker. The phenotypic coefficient of variation showed ample variability for the traits viz., plant height (27.19%), stalk diameter (28.21%), single cane weight (48.97%), internode number (22.60%) and internode length (29.15%). Further, twenty nine sequence-tagged microsatellite site (STMS) markers generated 495 bands with an average of 14.06 polymorphic bands. The accessions specific bands in respect to specific marker combinations were identified. The Jaccard's similarity coefficients among these accessions ranged from 0.42 to 0.78 with an average of 0.58 and clustering using unweighted pair group method of arithmetic-average (UPGMA) showed two major clusters with subclusters. Similarly polulation structure analysis based Bayesian approach grouped the individuals into two subpopulations, with alpha value of 0.112. The study shows that S. spontaneum accessions collected from Arunachal Pradesh is highly diverse, most of them will be harbouring the genes for cold tolerance and biomass. The set of markers which produced specific bands for the specific accessions identified in the study will help in identification of the particular accessions. The accessions studied are potential source for cold tolerance and high biomass, the results obtained in the present study will definitely help in planning and utilising them in sugarcane improvement programme. [ABSTRACT FROM AUTHOR]

Restriction fragment length polymorphism (RFLP) of nifH gene with three endonucleases revealed three different nifH genotypes among twenty one indigenous Bradyrhizobium yuanmingense strains. The interactive symbiotic effectiveness on soybean cv. JS335, nodulation and plant growth of these B. yuanmingense strains were comparatively evaluated with B. japonicum ASR011 under greenhouse conditions. Significant variation in symbiotic potential among native B. yuanmingense strains was observed and few of them exhibited significantly superior symbiotic performance over B. japonicum ASR011 and B. yuanmingense CCBAU 61071 type strain. A considerable difference in nitrogen-fixing characteristics was detected among B. yuanmingense strains which shared identical nifH gene sequence. This, to our knowledge, is the first study on symbiotic effectiveness of B. yuanmingense strains obtained from nodules of soybean cultivated in India. The symbiotically efficient B. yuanmingense strains may have applications in the formulation of appropriate inocula to improve soybean crop yield in Indian soils. [ABSTRACT FROM AUTHOR]

Symbiotic effect of twenty one indigenous Bradyrhizobium yuanmingense strains obtained from nodules of soybean cultivated in India was comparatively evaluated with B. japonicum ASR011 on soybean cv. JS335 for improved nodulation and plant growth performance under greenhouse conditions. Significant variation in symbiotic potential among native B. yuanmingense strains was observed and few of them exhibited significantly superior symbiotic performance i.e. improved the shoot and root dry weights and shoot N content compared to non-inoculated plants and over B. japonicum inoculated plants. The symbiotically efficient B. yuanmingense strains may have applications in the formulation of appropriate inocula to improve soybean crop yield on Indian soils. [ABSTRACT FROM AUTHOR]

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, Erianthus arundinaceus 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., Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03867-7., Competing Interests: Conflict of interestThe authors have no relevant financial or non-financial interests to disclose., (© King Abdulaziz City for Science and Technology 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.)

Phosphorus deficiency highly interferes with plant growth and development. Plants respond to persistent P deficiency by coordinating the expression of genes involved in the alleviation of stress. Promoters of phosphate transporter genes are a great choice for the development of genetically modified plants with enhanced phosphate uptake abilities, which improve crop yields in phosphate-deficient soils. In our previous study, the sugarcane phosphate transporter PHT1;2 gene showed a significantly high expression under salinity stress. In this study, the Erianthus arundinaceus EaPHT1;2 gene was isolated and characterized using various in silico tools. The deduced 542 amino acid residues have 10 transmembrane domains, with a molecular weight and isoelectric point of 58.9 kDa and 9.80, respectively. They displayed 71-96% similarity with Arabidopsis thaliana , Zea mays , and the Saccharum hybrid. To elucidate the function of the 5' regulatory region, the 1.1 kb promoter was isolated and validated in tobacco transgenics under Pi stress. The EaPHT1;2 promoter activity was detected using a β-glucuronidase (GUS) assay. The EaPHT1;2 promoter showed 3- to 4.2-fold higher expression than the most widely used CaMV35S promoter. The 5' deletion analysis with and without 5' UTRs revealed a small-sized 374 bp fragment with the highest promoter activity among 5' truncated fragments, which was 2.7 and 4.2 times higher than the well-used CaMV35S promoter under normal and Pi deprivation conditions, respectively. The strong and short promoter of EaPHT1;2 with 374 bp showed significant expression in low-Pi-stress conditions and it could be a valuable source for the development of stress-tolerant transgenic crops.

Sugarcane is a C4 and agro-industry-based crop with a high potential for biomass production. It serves as raw material for the production of sugar, ethanol, and electricity. Modern sugarcane varieties are derived from the interspecific and intergeneric hybridization between Saccharum officinarum, Saccharum spontaneum , and other wild relatives. Sugarcane breeding programmes are broadly categorized into germplasm collection and characterization, pre-breeding and genetic base-broadening, and varietal development programmes. The varietal identification through the classic breeding programme requires a minimum of 12-14 years. The precise phenotyping in sugarcane is extremely tedious due to the high propensity of lodging and suckering owing to the influence of environmental factors and crop management practices. This kind of phenotyping requires data from both plant crop and ratoon experiments conducted over locations and seasons. In this review, we explored the feasibility of genomic selection schemes for various breeding programmes in sugarcane. The genetic diversity analysis using genome-wide markers helps in the formation of core set germplasm representing the total genomic diversity present in the Saccharum gene bank. The genome-wide association studies and genomic prediction in the Saccharum gene bank are helpful to identify the complete genomic resources for cane yield, commercial cane sugar, tolerances to biotic and abiotic stresses, and other agronomic traits. The implementation of genomic selection in pre-breeding, genetic base-broadening programmes assist in precise introgression of specific genes and recurrent selection schemes enhance the higher frequency of favorable alleles in the population with a considerable reduction in breeding cycles and population size. The integration of environmental covariates and genomic prediction in multi-environment trials assists in the prediction of varietal performance for different agro-climatic zones. This review also directed its focus on enhancing the genetic gain over time, cost, and resource allocation at various stages of breeding programmes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Mahadevaiah, Appunu, Aitken, Suresha, Vignesh, Mahadeva Swamy, Valarmathi, Hemaprabha, Alagarasan and Ram.)

Background: Sheath rot disease caused by Sarocladium oryzae is an emerging threat for rice cultivation at global level. However, limited information with respect to genomic resources and pathogenesis is a major setback to develop disease management strategies. Considering this fact, we sequenced the whole genome of highly virulent Sarocladium oryzae field isolate, Saro-13 with 82x sequence depth., Results: The genome size of S. oryzae was 32.78 Mb with contig N50 18.07 Kb and 10526 protein coding genes. The functional annotation of protein coding genes revealed that S. oryzae genome has evolved with many expanded gene families of major super family, proteinases, zinc finger proteins, sugar transporters, dehydrogenases/reductases, cytochrome P450, WD domain G-beta repeat and FAD-binding proteins. Gene orthology analysis showed that around 79.80 % of S. oryzae genes were orthologous to other Ascomycetes fungi. The polyketide synthase dehydratase, ATP-binding cassette (ABC) transporters, amine oxidases, and aldehyde dehydrogenase family proteins were duplicated in larger proportion specifying the adaptive gene duplications to varying environmental conditions. Thirty-nine secondary metabolite gene clusters encoded for polyketide synthases, nonribosomal peptide synthase, and terpene cyclases. Protein homology based analysis indicated that nine putative candidate genes were found to be involved in helvolic acid biosynthesis pathway. The genes were arranged in cluster and structural organization of gene cluster was similar to helvolic acid biosynthesis cluster in Metarhizium anisophilae. Around 9.37 % of S. oryzae genes were identified as pathogenicity genes, which are experimentally proven in other phytopathogenic fungi and enlisted in pathogen-host interaction database. In addition, we also report 13212 simple sequences repeats (SSRs) which can be deployed in pathogen identification and population dynamic studies in near future., Conclusions: Large set of pathogenicity determinants and putative genes involved in helvolic acid and cerulenin biosynthesis will have broader implications with respect to Sarocladium disease biology. This is the first genome sequencing report globally and the genomic resources developed from this study will have wider impact worldwide to understand Rice-Sarocladium interaction.