Genetic diversity and population structure among 133 elite genotypes of sugarcane (Saccharum spp.) for use as parents in sugarcane varietal improvement

Genetic diversity and population structure of sugarcane introgressed hybrids by SSR markers

One hundred and seventy two introgressed hybrids from four different introgression groups and in three nobilized stages (F1, BC1,and BC2) involving two genera viz., Sugarcane (Saccharum spp) and Erianthusl (E.arundinaceus),and Coimbatore (Commercials) clones were studied for yield and quality traits, and as well with 30 SSR markers (simple sequence repeats) for diversity and population structure. The yield and quality components of the introgressed hybrids from improved S. spontaneum, improved S. robustum, S. barberi (Pathri) and E. arundinaceus (IK-76-76) showed significant variation. The traits viz., cane height, single cane weight and cane yield showed the highest level of phenotypic and genotypic variation. 456 polymorphic alleles in all with values ranging from 6 (SMC 863-GC) to 24 (NKS 43) with an average of 15 alleles per primer were studied. Polymorphism information content (PIC) generated by 30 SSR primers varied from 0.57 (NKS 1) to 0.94 (NKS 34) and the highest average PIC (0.93) was observed in hybrids of S. spontaneum (SSH). The highest number of observed and effective alleles, and Shannon's index were also registered by introgressed hybrids of SSH and the lowest variability was observed with hybrids of Co canes x S. barberi. SSR-based population genetic measures identified three mating groups involving improved S.officinarum, improved S.robustum and Coimbatore canes with maximum variability. Structure analysis identified 51 introgressed hybrids with abundant genetic variation and low gene flow as a new germplasm source for future sugarcane breeding programmes. Fifty-nine rare alleles were detected, and structure analysis revealed a low degree of admixture between the generated hybrids. Low gene flow estimates from group I (Nm: 1.052, where mostly F1 and BC1 hybrids were grouped together) explained that the maximum variability from parental clones was inherited until the BC1 generation, and high values of Nm in group III also indicated that most of the wild alleles were fixed in the BC1 population. Structure and cluster analysis (PCoA, UPGMA) explained that the grouping of introgressed hybrids is highly correlated to different stages of nobilization. UPGMA and PCoA methods grouped the individuals into three major clusters, with a clear differentiation of F1 and backcross hybrids grouped under different internal sub-clusters. The occurrence of wide genetic variability in the population and elite hybrids with a unique genetic base can be exploited in breeding programmes to develop trait specific donors for genetic enhancement and to mitigate climate change.

Genetic diversity assessment of Hopea hainanensis in Hainan Island

Hopea hainanensis (Dipterocarpaceae) is an endangered tree species restricted to Hainan Island, China, and a small part of Northern Vietnam. On Hainan Island, it is an important indicator species for tropical forests. The wood of Hopea hainanensis has a very high utilization value in nature since it is compact in structure, hard in texture, not easily deformed after drying, durable, and resistant to sunlight and water. As a result of its high quality, it has been felled and mined by humans without restraint, resulting in a reduction of its population size, severe habitat fragmentation, and a sharp decline in its population. Therefore, its conservation biology needs to be researched urgently. Researchers are currently focusing on the ecological factors and seed germination in the habitat of Hopea hainanensis to determine its endangered status. In the literature, there are no systematic analyses of the endangered mechanism of Hopea hainanensis in terms of genetic diversity. It focuses especially on the systematic genetic diversity of Hopea hainanensis in fragmented habitats. Using single nucleotide polymorphism (SNP) and genotyping-by-sequencing (GBS) technology, 42 samples from seven different cohabitation groups were genotyped. The results showed that the average heterozygosity of the six populations of Hopea hainanensis was 19.77%, which indicated that the genetic diversity of Hopea hainanensis was low. Genetic diversity research is essential for rare and endangered plant protection research. We can find a scientific basis for protecting endangered plants on slope bases by analyzing genetic differences and relationships among populations.

Identification of potential MTAs and candidate genes for juice quality- and yield-related traits in Saccharum clones: a genome-wide association and comparative genomic study

Sugarcane is an economically important commercial crop which provides raw material for the production of sugar, jaggery, bioethanol, biomass and other by-products. Sugarcane breeding till today heavily relies on conventional breeding approaches which is time consuming, laborious and costly. Integration of marker-assisted selection (MAS) in sugarcane genetic improvement programs for difficult to select traits like sucrose content, resistance to pests and diseases and tolerance to abiotic stresses will accelerate varietal development. In the present study, association mapping approach was used to identify QTLs and genes associated with sucrose and other important yield-contributing traits. A mapping panel of 110 diverse sugarcane genotypes and 148 microsatellite primers were used for structured association mapping study. An optimal subpopulation number (ΔK) of 5 was identified by structure analysis. GWAS analysis using TASSEL identified a total of 110 MTAs which were localized into 27 QTLs by GLM and MLM (Q + K, PC + K) approaches. Among the 24 QTLs sequenced, 12 were able to identify potential candidate genes, viz., starch branching enzyme, starch synthase 4, sugar transporters and G3P-DH related to carbohydrate metabolism and hormone pathway-related genes ethylene insensitive 3-like 1, reversion to ethylene sensitive1-like, and auxin response factor associated to juice quality- and yield-related traits. Six markers, NKS 5_185, SCB 270_144, SCB 370_256, NKS 46_176 and UGSM 648_245, associated with juice quality traits and marker SMC31CUQ_304 associated with NMC were validated and identified as significantly associated to the traits by one-way ANOVA analysis. In conclusion, 24 potential QTLs identified in the present study could be used in sugarcane breeding programs after further validation in larger population. The candidate genes from carbohydrate and hormone response pathway presented in this study could be manipulated with genome editing approaches to further improve sugarcane crop.

Response of Sugarcane Rhizosphere Bacterial Community to Drought Stress

Sugarcane is an important sugar and energy crop, and its yield is greatly affected by drought. Although a large number of studies have shown that rhizosphere microorganisms can help improve the adaptability of plants to biotic or abiotic stresses, there is a lack of studies on the adaptability of sugarcane rhizosphere microbial communities to host plants. Therefore, we conducted drought stress treatment and normal irrigation treatment on three sugarcane varieties GT21, GT31, and GT42 widely cultivated in Guangxi. Using 16S rDNA sequencing technology to analyze the changes in abundance of the sugarcane rhizosphere bacterial community under different treatments, combined with the determination of soil enzyme activity, soil nutrient content, and sugarcane physiological characteristics, we explored the sugarcane rhizosphere bacterial community response to drought stress. In addition, we used the structural equation model to verify the response path of sugarcane rhizosphere bacteria. The results show that the bacterial community structure in the rhizosphere of sugarcane is stable under normal water conditions. The change in the bacterial community structure under drought stress has a 25.2% correlation with the drought adaptability of sugarcane, but the correlation with drought stress is as high as 42.17%. The changes in abundance of rhizosphere bacteria under drought stress are mainly concentrated in the phylum Rhizobiales and Streptomycetales. This change is directly related to the physiological state of the host plant under drought stress, soil available phosphorus, soil urease and soil acid protease. We investigated the response species of rhizosphere microorganisms and their response pathways under drought stress, providing a scientific basis for rhizosphere microorganisms to assist host plants to improve drought adaptability.