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Abstract Sugarcane root system comprises of superficial sett roots as well as deeply-penetrating shoot borne roots (SBR) with latter being the permanent root system. In sugarcane, the healthy SBR contributes to a better crop yield and it also helps to produce multiple ratoon crops after the harvest. There is a dearth of in-depth knowledge on SBR system architecture and its functional role in modern day commercial hybrids. A comprehensive phenotypic, anatomical and whole transcriptome profiling, conducted between the commercial sugarcane hybrids and a wild germplasm Erianthus, found a developmental delay in both initiation and establishment of the SBR in commercial hybrid compared to Erianthus. The SBR system in Erianthus proved to be an extensive drought-adaptive root system architecture that significantly contributes to drought tolerance. On the other hand, SBRs in the commercial hybrids showed an irreversible collapse and damage of the root cells under drought stress. The outcomes from the comparative analysis of the transcriptome data showed a significant upregulation of the genes that regulate important stress signalling pathways viz., sugar, calcium, hormone signalling and phenylpropanoid biosynthesis in the SBRs of Erianthus. It was found that through these key signalling pathways, Erianthus SBRs triggered the downstream signalling cascade to impart physiological responses like osmoprotection, modification of the cell walls, detoxification of reactive oxygen species, expression of drought responsive transcription factors, maintenance of cell stability and lateral root development. The current study forms a basis for further exploration of the Shoot Borne Root system as a valuable breeding target to develop drought tolerant sugarcane genotypes.

Abstract Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na+/K+, Ca2+/K+ and Mg2+/K+ ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR

Abstract Sugarcane is a trans-seasonal long-duration crop and tillering phase (60–150 days) is the most sensitive phase for moisture stress, causing significant reduction in biomass accumulation. The study focussed to assess the Genotype × Environment Interaction (GEI) for tillering phase moisture stress and to identify the stable genotypes in sugarcane. The study dealt with 14 drought tolerant genotypes and two standards (Co 86032 and CoM 0265) which were evaluated in two plant and one ratoon trials at four locations in Maharashtra, India. The moisture stress was imposed for 60 days from 90 to 150 days after planting and corresponded to tillering phase by withholding the irrigation. The AMMI ANOVA showed significant GEI for cane and CCS yield accounting 18.33 and 19.45 percent of variability respectively. Drought and genotype main effects were highly significant accounting 49.08 and 32.59 percent variability for cane yield and, 52.45 and 28.10 percent variability for CCS yield respectively. The first two interactive principal component (IPCA) biplots of AMMI showed diverse nature of all four environments and the Discriminative vs Mean biplots of Genotype + genotype × environment interaction (GGE) model showed that ‘Pune’ as the highly discriminating environment. The genotype ranking biplots of GGE showed that Co 85019 was the most stable genotype followed by Co 98017. Similar results were also observed in Yield vs IPCA1 biplot of AMMI, which revealed Co 85019 and Co 98017 as high yielding stable varieties. Yield related environmental maximum (YREM) showed thirteen and nine percent loss due to crossover interactions in Co 85019 for cane yield and CCS yield respectively. The multi-environment BLUP and genotype stability index (GSI) has reaffirmed that Co 85019 as a drought proof and stable genotype with high yield under tillering phase drought stress. The results suggested using Co 85019 for cultivation in drought prone regions and the usefulness of the methodology for identifying more such sugarcane varieties for the benefit of resource poor famers in drought affected regions.

In the context of horticulture's crucial role in economic growth, nutritional security and employment, the sector faces challenges related to dissemination of credible scientific information, particularly in rural areas. The gap in information access leads farmers to rely on experiential knowledge and peer opinions. Leveraging information and communication technology (ICT), specifically quick response (QR) codes, presents an innovative solution to bridge this information gap. This paper investigates stakeholders' awareness, utilization, size and display distance and constraints in utilizing QR codes for accessing horticultural information. The findings indicated that 93.33% of the respondents reported previous usage, highlighting the technology's ubiquity and acceptance. Moreover, stakeholders expressed positive inclination towards QR code adoption for accessing horticultural information, with 53.33% expressing likelihood to embrace QR technology. Effect of QR code size on the display board and their display distance on the usability and adoption was also studied, which indicated, 71.22% accessed QR codes on large displays of size 8" x 11", while, 16.66% accessed them on small displays of size 4" x 5". However, despite the positive reception, several challenges impede QR code utilization. Poor internet network connectivity (mean score: 71.00) during National Horticultural Fair (NHF-2024) emerges as a significant barrier, alongside entrenched preferences for traditional methods (mean score: 69.00). By aligning QR code designs with stakeholders' preferences and addressing constraints, horticultural stakeholders can leverage QR codes more effectively, fostering knowledge dissemination and driving horticultural development. [ABSTRACT FROM AUTHOR]

Cowpea (Vigna unguiculata) is a self-pollinating grain legume, fodder, and vegetable crop grown in a variety of tropical and subtropical climates around the world. Due to its nutritive value and soil-improving properties, it is also used as a fodder, green manure and cover crop. Being a legume crop, cowpea fits well in the inter-cropping system. Many biotic stresses, such as diseases caused by fungi, bacteria and viruses, significantly affect the crop yield in cowpeas. Apart from these, abiotic stresses such as drought, salinity stress and cold stresses are emerging problems. Therefore, it is required to breed many resistant varieties or genotypes through the identification of resistant gene pools. Vegetable cowpea breeding programs aim to develop cowpea varieties for vegetable purposes with tender pods in a bush or semi-determinate growth habits. Besides the development of high-yielding varieties, resistance to diseases such as golden mosaic disease, Cercospora leaf spot and anthracnose, resistance to insect pests such as bruchids pod borer and tolerance to abiotic stresses such as drought, salinity and high-temperature stresses is important. To achieve this traditional breeding combined with molecular approaches such as marker-assisted selection and genomic selection increases the precision of selection for desirable traits and also aids in the development of varieties with combined resistance to two or more diseases in less time. Genomic prediction and genomic selection schemes in cowpeas showed considerable improvement in predication accuracies and integrating with breeding schemes helps to enhance genetic gain. [ABSTRACT FROM AUTHOR]

The utilization of superior parental lines and identification of superior families enhance the genetic gain in sugarcane. To identify the superior parental lines and superior progenies, 1889 progenies derived from twenty crosses involving genetically diverse historical parents were evaluated for juice quality and yield attributing traits.The historical parental lines were selected based on coefficient of coancestry from the tropical and subtropical parents maintained at National Hybridization Garden. Based on progeny performance, families of Co 99006 × CoSe 92423 and Co 86032 × 85R186 were found superior for number of millable canes, , Co 86032 × 85R186 and Co 8371 × CoT 8201 for cane thickness and CoSe 95422 × Co 775 and Co 8371 × CoV 92102 for sucrose content. Parental lines such as Co 86002, Co 99006 and CoLk 98184, Co 775, 85R186 and BO 130 were identified for HR Brix; Co 419 and Co 89010, CoS 510, CoV 92102 and CoSe 92423 for cane thickness; and CoLk 94184, BO 91 and BO 32 for number of millable canes. The estimates of coefficient of coancestry was negatively correlated with HR Brix and cane thickness suggesting that parental cross combination with lesser value of coefficient of coancestry or inbreeding coefficient resulted in produce the heterotic progenies. This study based on the historic parental lines selected based on the coefficient of coancestry and inference limited to only to this experimental material. The evaluation of families derived from the population parental cross combination and parental lines in replication family block design permits the estimation of BLUP based breeding values and helpful in selection of superior parental lines and superior progenies.

Field experiments were conducted during 2016-17 and 2017-18 crop seasons with twenty test clones viz., Co 0238, Co 0240, Co 06031, Co 09004, Co 11015, Co 13001, Co 13003, Co 13006, Co 13014, Co 13018, Co 13020, Co 13021, Co 14008, Co 14016, Co 14026, Co 15005, Co 15007, Co 15021, Co 16001 and Co 16002 along with three standards viz., Co 86032, Co 0212 and Co 06030 at Ponni Sugar Ltd, Odapalley. On the basis of pooled mean of two plant crop trials and a ratoon trial, clones such as Co 09004, Co 11015, Co 16002 and Co 13001 were identified as early high sucrose clones suitable for early crushing. These clones may be used as potential donors in the hybridization programme for transferring extra earliness and high sucrose trait in high yielding commercial varieties. Based on juice quality characteristics at 300 days and 360 days Co 15007 was identified as mid-late maturing clones. The ratoon performance of Co 14016 was excellent. Co 14016 which recorded significantly higher cane yield (184.72 t/ha) and sugar yield (23.17 t/ha) than the standard Co 86032 (134.02 and 17.73 t/ha respectively) may be used as a parental source for crossing with extra early maturing varieties to improve cane yield and ratoon performance. On the basis of the cane yield and sugar yield at harvest, Co 13014 and Co 15007 were found better than Co 86032. Based on the juice quality traits, Co 15005 and Co 15007 were identified as typical mid-late clones. The variety Co 11015 registered 6.79, 7.56 and 7.02 per cent improvement in sucrose % at 240, 300 and 360 DAP, respectively over Co 86032 which is a remarkable improvement in sugarcane. The mean CCS yield (19.27 t/ha) of Co 11015 was at par with that of the standard Co 86032 (20.54). Therefore, large scale cultivation of this extra early high sugar variety Co 11015 in the north-western region of Tamil Nadu is suggested for improving sugar recovery and profit of the farmers.

A DESCRIPTION OF Co 11015 (ATULYA) A RECENTLY NOTIFIED SUGARCANE VARIETY FOR TAMIL NADU

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 root system comprises of superficial sett roots as well as deeply-penetrating shoot borne roots (SBR) with latter being the permanent root system. In sugarcane, the healthy SBR contributes to a better crop yield and it also helps to produce multiple ratoon crops after the harvest. There is a dearth of in-depth knowledge on SBR system architecture and its functional role in modern day commercial hybrids. A comprehensive phenotypic, anatomical and whole transcriptome profiling, conducted between the commercial sugarcane hybrids and a wild germplasm Erianthus, found a developmental delay in both initiation and establishment of the SBR in commercial hybrid compared to Erianthus. The SBR system in Erianthus proved to be an extensive drought-adaptive root system architecture that significantly contributes to drought tolerance. On the other hand, SBRs in the commercial hybrids showed an irreversible collapse and damage of the root cells under drought stress. The outcomes from the comparative analysis of the transcriptome data showed a significant upregulation of the genes that regulate important stress signalling pathways viz., sugar, calcium, hormone signalling and phenylpropanoid biosynthesis in the SBRs of Erianthus. It was found that through these key signalling pathways, Erianthus SBRs triggered the downstream signalling cascade to impart physiological responses like osmoprotection, modification of the cell walls, detoxification of reactive oxygen species, expression of drought responsive transcription factors, maintenance of cell stability and lateral root development. The current study forms a basis for further exploration of the Shoot Borne Root system as a valuable breeding target to develop drought tolerant sugarcane genotypes., (© 2023. Springer Nature Limited.)

Erianthus arundinaceus [Retzius] Jeswiet, a wild relative of sugarcane has a high biomass production potential and a reservoir of many genes for superior agronomic traits and tolerance to biotic and abiotic stresses. A comparative physiological, anatomical and root transcriptome analysis were carried out to identify the salt-responsive genes and metabolic pathways associated with salt-tolerant E. arundinaceus genotype IND99-907 and salinity-sensitive sugarcane genotype Co 97010. IND99-907 recorded growth of young leaves, higher proline content, higher relative water content, intact root anatomical structures and lower Na + /K + , Ca 2+ /K + and Mg 2+ /K + ratio as compared to the sugarcane genotype Co 97010. We have generated four de novo transcriptome assemblies between stressed and control root samples of IND99-907 and Co 97010. A total of 649 and 501 differentially expressed genes (FDR<0.01) were identified from the stressed and control libraries of IND99-907 and Co 97010 respectively. Genes and pathways related to early stress-responsive signal transduction, hormone signalling, cytoskeleton organization, cellular membrane stabilization, plasma membrane-bound calcium and proton transport, sodium extrusion, secondary metabolite biosynthesis, cellular transporters related to plasma membrane-bound trafficking, nucleobase transporter, clathrin-mediated endocytosis were highly enriched in IND99-907. Whereas in Co 97010, genes related to late stress-responsive signal transduction, electron transport system, senescence, protein degradation and programmed cell death, transport-related genes associated with cellular respiration and mitochondrial respiratory chain, vesicular trafficking, nitrate transporter and fewer secondary metabolite biosynthetic genes were highly enriched. A total of 27 pathways, 24 biological processes, three molecular functions and one cellular component were significantly enriched (FDR≤ 0.05) in IND99-907 as compared to 20 pathways, two biological processes without any significant molecular function and cellular components in Co 97010, indicates the unique and distinct expression pattern of genes and metabolic pathways in both genotypes. The genomic resources developed from this study is useful for sugarcane crop improvement through development of genic SSR markers and genetic engineering approaches., (© 2021. The Author(s).)

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.)

Sugarcane is a trans-seasonal long-duration crop and tillering phase (60-150 days) is the most sensitive phase for moisture stress, causing significant reduction in biomass accumulation. The study focussed to assess the Genotype × Environment Interaction (GEI) for tillering phase moisture stress and to identify the stable genotypes in sugarcane. The study dealt with 14 drought tolerant genotypes and two standards (Co 86032 and CoM 0265) which were evaluated in two plant and one ratoon trials at four locations in Maharashtra, India. The moisture stress was imposed for 60 days from 90 to 150 days after planting and corresponded to tillering phase by withholding the irrigation. The AMMI ANOVA showed significant GEI for cane and CCS yield accounting 18.33 and 19.45 percent of variability respectively. Drought and genotype main effects were highly significant accounting 49.08 and 32.59 percent variability for cane yield and, 52.45 and 28.10 percent variability for CCS yield respectively. The first two interactive principal component (IPCA) biplots of AMMI showed diverse nature of all four environments and the Discriminative vs Mean biplots of Genotype + genotype × environment interaction (GGE) model showed that 'Pune' as the highly discriminating environment. The genotype ranking biplots of GGE showed that Co 85019 was the most stable genotype followed by Co 98017. Similar results were also observed in Yield vs IPCA1 biplot of AMMI, which revealed Co 85019 and Co 98017 as high yielding stable varieties. Yield related environmental maximum (YREM) showed thirteen and nine percent loss due to crossover interactions in Co 85019 for cane yield and CCS yield respectively. The multi-environment BLUP and genotype stability index (GSI) has reaffirmed that Co 85019 as a drought proof and stable genotype with high yield under tillering phase drought stress. The results suggested using Co 85019 for cultivation in drought prone regions and the usefulness of the methodology for identifying more such sugarcane varieties for the benefit of resource poor famers in drought affected regions., (© 2021. The Author(s).)

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.