Tropical Plant Biology

Supritha, D. S. Raj; Patil, Rajesh S.; Kasturi, Sai Valli Harshini; Patil, Bhuvaneshwara R.

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09373-1

Earliness in cotton is a highly valued trait that allows the crop to dodge late-season stress and facilitates efficient harvesting, ultimately benefiting farmers with optimal yield. Understanding the genetics of these complex traits is a prelude to designing extra-early maturing cotton genotypes. Two crosses with six generations (ESS-20 × FLT-25 and S-32 × FLT-25: P1, P2, F1, F2, BC1P1, and BC1P2) and one cross with five generations (NNDC-30 × NNDC-47: P1, P2, F1, F2, and F2:3) were field-evaluated for ten earliness and plant architecture traits in cotton. ANOVA presented significant generational differences for most traits. The inadequacy of the Additive-Dominance (A-D) model in explaining trait inheritance using scaling and joint-scaling tests highlighted the presence of epistatic gene actions. Further, the analysis of gene action unveiled the predominance of dominance effect [h] and dominance × dominance [l] epistatic effect, influencing the expression of most traits. Contrasting signs of [h] and [l] effects for these traits suggested the occurrence of duplicate epistasis across crosses. Therefore, population improvement strategies and heterosis breeding could be effective in designing extra-early maturing genotypes. All traits exhibited quantitative inheritance, with partial and overdominance favouring early maturity. Notably, days to flowering and boll opening, exhibited negative heterosis, suggesting the efficient development of short-duration cotton hybrids. Besides, the study also predicted less than one gene block for the majority of traits, suggesting a significant role of complex non-allelic interaction in trait expression. These findings offer valuable insights for strategizing efficient breeding methods to develop early-maturing cotton genotypes.

França, Vitória Costa Pereira Lopes Alves de; Campos, Wellington Ferreira; Cangussú, Luanna Vanessa de Souza; da Silva, Tânia Pires; Dobbss, Leonardo Barros

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09378-w

Soil salinity imposes severe stress on plant growth and limits crop yield, while humic acids (HA) promote plant growth and mitigate different abiotic stresses. HA has auxin-like activity, but the involvement of ethylene signaling in their action is poorly investigated. Moreover, whether the mitigating action of HA in the salt stress responses depends on ethylene is unclear. Thus, this work aimed to investigate whether (i) the humic substances mitigate the effects of salt stress on cultivated tomatoes and (ii) the action of humic acids depends on ethylene perception. To do that we used a genetic approach through wild-type (WT) MICRO-TOM (Solanum lycopersicum) and the ethylene insensitive Never ripe (Nr) mutant. Our data showed that HA promotes root growth of WT and Nr plants. The number of lateral roots, the main morphological marker of HA activity, decreased respectively, 33% and 18%, in WT and Nr plants under NaCl alone, while HA alone stimulated them in 7% (in WT) and 12% (in Nr), both compared to control conditions. The inhibitory effect of salt stress on the number of lateral roots was not observed when WT and Nr plants were simultaneously treated with HA and NaCl (HA + NaCl) which was significantly equal to those under control conditions. HA activity also mitigates the inhibitory effects of salt stress on photosynthesis of WT and Nr plants. Specifically, compared to the control, the relative chlorophyll content increased about 1.77 and 2.44 times, respectively, in WT and Nr plants in the HA + NaCl combination. Moreover, the increase in light absorption capacity was followed by increased photosystem II quantum yield and non-photochemical exciton quenching. Therefore, photochemical analysis demonstrated that HA promotes photosynthetic activity and reduces photodamage, in either unstressed or salt-stressed plants, and either WT or Nr plants. Overall, through a genetic approach, our data demonstrated that HA promotes plant growth independent of ethylene perception, as well as mitigates the inhibitory effects of salt stress.

Durai, A. Anna; Amaresh, ; Kumar, R. Arun; Hemaprabha, G.

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09372-2

Stable, and high yielding genotype with superior quality across the spatial and temporal variation are to be identified due to changing weather conditions which largely influences the true genotypic performance. The present experiment was conducted with 13 clones including seven test entries along with six recently released varieties as first plant, second plant and ratoon in RBD with three replications during the year 2022-23 and 2023-24 at ICAR-SBI, Coimbatore. Combined ANOVA revealed that there was a significant genotype main effects, environment main effects and G X E interaction effect for all the traits under study except for the traits, cane diameter and single cane weight for which environment main effects were not significant. The AMMI ANOVA for the sucrose, CCS percent, cane yield and CCS yield showed that significant individual effects of Genotypes, Environments and genotype × environment interaction. AMMI biplot analysis revealed that the genotypes Co 17,001, CoC 13,339 and Co 86,032 for cane yield and Co 86,032 and CoC 13,339 for CCS yield were stable. AMMI stability parameters such as ASV, MASV identified Co 86,032, Co 15,003, and CoC 13,339 were stable for cane and CCS yield. The GSI, EV, SIPC showed Co 17,001, Co 15,003, Co 86,032 and Co 11,015 were stable for cane and CCS yield. Multi-trait stability analysis considering the traits like sucrose, CCS percent, cane yield, CCS yield revealed that the genotypes Co 15,003 and Co 86,032 were highly stable. GGE analysis such as mean vs. stability, ranking of genotypes, which won where biplots pinpointed that the genotype Co 17,001 is highly stable than the standards Co 11,015 and Co 86,032 for sucrose content, cane and CCS yield. Thus, the genotypes Co 17,001 and Co 15,003 were stable and superior than the commercial varieties like Co 11,015 and Co 86,032 according to the AMMI, AMMI stability parameters and GGE for the cane yield and CCS yield and they may be promoted for commercial cultivation in target environment. These promising genotypes should be further evaluated in multi-diverse environments across the country to confirm their stability and potential for commercial cultivation in farmers field.

Souza, Juliana Lopes; Nunes, Valdinete Vieira; Freitas, Bruno Antonio Lemos de; Santos, Heloisa Oliveira dos; Silva-Mann, Renata

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09377-x

Storage of desiccation-tolerant seeds is one of the most effective germplasm conservation strategies; however, various species from tropical and subtropical humid forests have seeds that are sensitive to desiccation, recalcitrant seeds, making conservation a challenge. Recalcitrant seeds deteriorate during storage due to high respiration rates and metabolic activity, and protocols employing osmoprotective solutions aim to minimize those effects to maintain seed viability for a longer period. Hancornia speciosa, a fruit tree considered a priority for research in Brazil, is a desiccation-sensitive species of biannual harvest. Thus, the objective of this study was to assess the physiological parameters of viability, vigor, and enzymatic activity of H. speciosa seeds of two harvest seasons, stored in an osmoprotective solution. Germination percentage, water content, electrical conductivity, shoot, root, and seedling length, peroxidase concentration, and heat-resistant protein concentration were all determined for seeds collected during the summer and winter harvests. In addition, gene sequences were explored through gene ontology using Blast analysis to identify the biological and molecular processes associated with enzymatic action during storage. Summer-collected seeds performed better in terms of viability and vigor, with the highest development of shoot, root, and seedling length. The summer-harvest seeds had an initial germination of 80% and maintained a 15% germination rate until 90 days of storage. The seeds collected in the winter had lower initial germination and vigor; however, improved in those parameters during storage in the protective solution, with an increase of 12.5% in germination rate after 90 days. H. speciosa seeds harvested in the summer or winter and stored in the osmoprotective solution remain viable for up to 90 days. The solution has an osmopriming effect on low-vigor seeds, increasing viability and vigor, and the summer-harvest seeds are recommended for storage in the osmoprotective solution. Peroxidase and heat-resistant proteins are active during storage in the solution; the regulation of the expression of these enzymes should be investigated further.

Kumari, Priyanka; Dhall, Rajinder Kumar; Lnu, Ritika; Singathiya, Prakash; Praveen, S.; Manchanda, Pooja

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09390-0

The present research was carried with the objective to develop parthenocarpic gynoecious cucumber hybrids that exhibit high yield, better quality and early maturing. These hybrids could potentially be approved for widespread commercial cultivation within the state. To achieve this goal, it is essential to estimate the heterotic pattern of cucumber hybrids for improvement in yield and quality traits. The experiment was comprised of five lines (gynoecious, parthenocarpic), eleven testers (monoecious) to develop 55 F1 hybrids and one standard check ‘Rajani’ using line x tester mating design. The average heterosis, standard heterosis and specific combining ability (SCA) were estimated in cucumber cross combinations for eleven different yield and quality traits. For fruit yield, magnitude of standard heterosis, average heterosis and SCA ranged from -66.02% to 6.8%, -41.73% to 123.35%, -0.60 to 0.66 respectively. On the basis of per se performance, SCA, average heterosis and standard heterosis crosses, 25–16 VNR x PMC-1, 25–16 VNR x AVCU-1203, PK-1 × PMC-1, PBRK-11 × Punjab Naveen, PK-1 × Punjab Naveen were found best for fruit yield, fruit number, fruit length, fruit weight and diameter. The earliness was judged by days to first fruit picking and node at which first female flower appears and crosses 25–16 VNR x PMC-1 and PBRK-11 × Swarna Ageti was found early maturing. For fruit quality, AVCU-1303 × Swarna Sheetal and AVCU-1303 × AVCU-1202 were found best. So, these hybrids could be used for commercial release.

Sahoo, Raj Kishore; Swain, Nibedita; Selvaraj, Sabarinathan; Nayak, Gyanisha; Sarkar, Suman; Singh, Nihar Ranjan; Parameswaran, C.; Behera, Biswaranjan; Samantaray, Sanghamitra

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09370-4

Haplotype breeding assists in improvement of traits through introgression of superior haplotypes. Growth Regulating Factor 4 (GRF4) regulates yield and nitrogen use efficiency in rice. Further, through regulation of MYB61, GRF4 also regulates the plant biomass in rice. However, the trait effects of different GRF4 haplotypes on yield and biomass relationship is not understood properly. This study hypothesised that GRF4 haplotypes affects the yield and biomass relationship and studied the haplotype differences of GRF4 in 335 rice accessions for yield and biomass relationship. Fixation index (Fst) of GRF4 haplotypes were found to be higher (0.31) between indica and japonica as compared to indica and aus (0.18), japonica and aus ecotypes (0.18). Further, marker trait association identified five significant associations one for flag leaf length (Chr02:28862688), two each for biomass (Chr02:28862385, Chr02:28868744) and grain number (Chr02:28861294, Chr02:28863481), and one for seed yield per plant (Chr02:28868744). Among the traits associated with haplotypes, Hap4 showed higher yield and biomass relationship (r2 = 0.82), whereas the superior haplotype for yield (Hap1) showed relatively lesser biomass and yield relationship (r2 = 0.60). Besides, two favourable SNPs regulating grain number and non-favourable SNP for flag leaf width was fixed in the IRRI elite lines and popular rice varieties. This indicates yield and biomass relationship between the GRF4 haplotypes varies in the rice genotypes. Further, balancing the breeding or genome editing strategies for yield and biomass has potential for genetic improvement in rice.Graphical Abstract[graphic not available: see fulltext]

Xiao, Ling; Cai, Xiaowei; Yu, Runrun; Nie, Xiangmei; Wang, Ai-Hua; Yang, Kun; Wen, Xiaopeng

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09369-x

Pitaya is a widely cultivated crop in Southeast Asia with excellent performance against drought stress. The fruits are of great economic value, which draws increasing attention and promotes the plantation extension in China. Presently, a genome-wide identification of the TCP genes was conducted in pitaya. Their physiochemical properties, genome collinearity, phylogenetic relationship, biological functions, cis-acting elements and expression pattern were analyzed. The results showed that pitaya genome codes a total of 24 TCP transcription factors, among which 12 belong to Class I and 12 to Class II. Phylogenetic and collinearity analysis revealed that HpTCPs are phylogenetically close to those of Beta vulgaris; the expansion of pitaya TCPs may be attributed to the segmental and dispersed duplications occurred after the divergence of dicots and monocots. Moreover, the Ka/Ks ratio suggested that HpTCPs are under purifying selection. Gene ontology analysis and subcellular localization prediction indicated that most HpTCPs are located in nucleus involving in the transactivation of downstream genes, which was further verified through transient tobacco transformation experiments and modified yeast two-hybrid assays, performed on randomly selected genes, HpTCP10 and HpTCP24. Investigation of HpTCP promoters detected an abundance of phytohormone- and stress-responsive elements. Transcriptomic data indicated that HpTCPs, especially the Class II members, were predominantly expressed in floral buds and flowers, suggesting a significant association with flower development. Using RT-qPCR, the response to low-temperature and drought stresses was revealed for HpTCPs, among which HpTCP11 and HpTCP23 displayed the most robust up-regulation, indicating their positive involvement in the stress response of pitaya and therefore might be targets for genetic improvement of pitaya.

Umesha, M.; Sunisha, C.; Chandrashekar, N.; Usharani, T. R.; Sowmya, H. D.; Sriram, S.

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09383-z

Fusarium oxysporum f. sp. cubense (Foc) is a soil-borne pathogen that severely limits banana yields globally. In the present study, the Rasthali (AAB) banana cultivar was transformed with the Arabidopsis thaliana BAG4 gene, driven by a root-specific promoter, to modulate cell death pathways and induce resistance against the fungal pathogen. Stable transgenic plants were developed by transforming embryogenic cells derived from immature male floral buds. Integration and expression of the gene cassette in transformants were confirmed by Southern blotting and real-time PCR, respectively. Stable transgenic banana lines were selected based on their copy number and vigorous growth. The root challenge bioassay of the selected lines showed a vascular discoloration index (VDI) ranging from 8 to 51%, compared to untransformed bananas, which exhibited a 97% VDI. Lines demonstrating tolerance were further micro-propagated for detailed analysis. The enzyme activities of superoxide dismutase and peroxidase were higher in transformed lines than control plants. Additionally, the TUNEL assay of the stable transformant line 168 exhibited reduced apoptotic-like features in the roots post-Foc infection. The results indicated that AtBAG4 transgenic Rasthali plants exhibited tolerance to Foc (Race 1) by inhibiting cell death. Therefore, AtBAG4 gene-mediated tolerance in banana cv. Rasthali offers a promising and sustainable approach for the integrated management of Fusarium wilt in bananas.

Vaishnavi, Kandasamy; Geetha, Seshadri; Boopathi, Narayanan Manikanda; Ganesan, Kalipatty Nalliappan; Uma, Doraiswamy; Anandhi, Krishnan

2025 Tropical Plant Biology

doi: 10.1007/s12042-025-09392-6

Flavonoids are key therapeutic compounds in rice. This study aimed to develop genetic stocks with high flavonoid content by analyzing 235 F5 rice lines derived from ADT48 (low flavonoid) x Kavuni (high flavonoid). The morphological, molecular and biochemical analysis of the F5 population revealed that the main flavonoid content in the donor parent was quercetin and respective genomic regions could be transferred to the high-yielding, low flavonoid parent background through recombination breeding. Further, a positive correlation was found between total flavonoid content and panicle length and hundred-seed weight, indicating the potential for simultaneous improvement of yield and flavonoid content. The SSR markers RM228 and RM5348 had R² values of 0.5439 and 0.1619, respectively. RM228 was found to have a high R2 and strong linkage with the candidate gene flavonol synthase and hence could be considered as the reliable SSR marker for selecting high flavonoid content progenies in early segregating generations. Three F5 recombinants were found to have elevated TFC with the appreciable performance of yield-related traits along with medium slender grains. This indicates that flavonoid content in rice can be enhanced through recombination breeding, without adversely affecting yield or grain quality.

Li, An-zi; Peng, Xin; Huang, Yuan; Bi, Zhao-fu; Liao, Ming-jing; Zhang, Mu-qing; Xiao, Sheng-hua

2025 Tropical Plant Biology

doi: 10.1007/s12042-024-09380-2

  The β-Ketoacyl-CoA synthase (KCS) plays a crucial role in the synthesis of very-long-chain fatty acids (VLCFAs), regulation of stress responses, and developmental processes. However, knowledge of this gene family in sugarcane is still limited. In this study, we identified 38 KCS genes in the Saccharum spontaneum genome. Phylogenetic analysis categorized these genes into four distinct subfamilies and collinearity analysis indicated that gene family expansion primarily occurred through genome-wide or fragment replication. Almost all SsKCS promoters contained ABA-responsive, MeJA-responsive, and light-responsive elements (G-box) that are involved in regulating plant hormones and stress responses. Most of them revealed higher expression levels in seedlings compared to mature tissues. SsKCS1/10/16/17/20/37 exhibited significantly higher expression levels in the drought-resistant compared with the drought-sensitive cultivar. Moreover, we found that the wax content and the expression levels of SsKCS5/9/10/37 were also higher in drought-resistance cultivar than in drought-sensitive cultivar. Together, the first systematic analysis of the KCS family in sugarcane broadens deeper insights into their evolutionary dynamics and functional properties, and potentially provides candidate genes for sugarcane genetic improvement.