Kittipat Ukoskit

Drought is a significant constraint to sugarcane productivity. Therefore, understanding how different varieties of sugarcane respond to drought stress can facilitate breeding programs and set up criteria for selecting drought-tolerant varieties. In the present study, we examined eight morpho-physiological traits to distinguish 40 sugarcane genotypes categorized into four groups based on significant differences in cane yield under non-stressed conditions and reduction of cane yield under drought-stressed conditions. The study was conducted during the formative stage in a greenhouse, encompassing both control and drought conditions. Drought treatments resulted in significant changes and differences in the mean values of various morpho-physiological traits. The hierarchical clustering analysis, utilizing stay-green traits such as higher chlorophyll fluorescence ratio (F_v/F_m), leaf chlorophyll content (SPAD), leaf relative water content (RWC), and lower leaf rolling score (LR), leaf drying score (LD), and drought recovery score (DR), successfully grouped 40 sugarcane genotypes into four major clusters, similar to the previously categorized groups. Correlation analysis showed significant relationships among cane yield, reduction of cane yield under drought conditions, and the stay-green traits. Our results demonstrated that morpho-physiological traits contributing to the “stay-green” phenotypes could be useful as selection criteria for drought tolerance in sugarcane.

Dissection of the genetic loci controlling drought tolerance traits with a complex genetic inheritance is important for drought-tolerant sugarcane improvement. In this study, we conducted a large-scale candidate gene association study of 649 candidate genes in a sugarcane diversity panel to identify genetic variants underlying agronomic traits and drought tolerance indices evaluated in plant cane and ratoon cane under water-stressed (WS) and non-stressed (NS) environments. We identified 197 significant marker-trait associations (MTAs) in 141 candidate genes associated with 18 evaluated traits with the Bonferroni correction threshold (α = 0.05). Out of the total, 95 MTAs in 78 candidate genes and 62 MTAs in 58 candidate genes were detected under NS and WS conditions, respectively. Most MTAs were found only in specific water regimes and crop seasons. These MTAs explained 7.93–30.52% of phenotypic variation. Association mapping results revealed that 34, 59, and 104 MTAs involved physiological and molecular adaptation, phytohormone metabolism, and drought-inducible genes. They identified 19 pleiotropic genes associated with more than one trait and many genes related to drought tolerance indices. The genetic and genomic resources identified in this study will enable the combining of yield-related traits and sugar-related traits with agronomic value to optimize the yield of sugarcane cultivars grown under drought-stressed and non-stressed environments.

Leptocybe invasa is a gall wasp causing significant damage to Eucalyptus species. This study used RNA sequencing (RNA-seq) to identify differentially expressed genes (DEGs) associated with early L. invasa infestation in eucalyptus parents and their F₁-progenies. A total of 14,648 significant DEGs were identified from U22-tolerant and C153-susceptible parents, and extremely tolerant and susceptible pools of their F₁-progenies. A total of 324/632 and 182/205 DEGs specific for the tolerant group and the susceptible group were up-regulated, respectively. Expression analysis by qRT-PCR of the selected DEGs was comparable with the results of RNA-seq. Expression analysis of the selected genes using the top five progenies from each pool was consistent with that in the parents. Three genes (RCA, SUI1, GCN5) were up-regulated after infestation in all tested tolerant plants, suggesting their important roles in the tolerant phenotype. Using expression and STRING analysis, our results suggest that early response at three days after gall wasp infestation increased protein and terpenoid synthesis, and increased transportation of these molecules. In addition, wounding also increased photosynthesis and glycolysis. These processes involved the interaction of several plant hormones, such as JA, Auxin, and ABA. The information obtained from this study could be useful for future Eucalyptus breeding programs.

Girth growth is an important factor in both latex and timber production of the rubber tree. In this study, we performed candidate gene association mapping for girth growth in rubber trees using intron length polymorphism markers (ILP) in identifying the candidate genes responsible for girth growth. The COBL064_1 marker developed from the candidate gene (COBL4) regulating cellulose deposition and oriented cell expansion in the plant cell wall showed the strongest association with girth growth across two seasons in the Amazonian population and was validated in the breeding lines. We then applied single molecule real-time (SMRT) circular consensus sequencing (CCS) to analyze a wider gene region of the COBL4 to pinpoint the single nucleotide polymorphism (SNP) that best explains the association with the traits. A SNP in the 3’ UTR showing linkage disequilibrium with the COBL064_1 most associated with girth growth. This study showed that the cost-effective method of ILP gene-based markers can assist in identification of SNPs in the candidate gene associated with girth growth. The SNP markers identified in this study added useful markers for the improvement of girth growth in rubber tree breeding programs.

Background: Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world’s largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs. Results: From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species. Conclusions: Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.