Analysis of the genetic structure and diversity of upland cotton groups in different planting areas based on SNP markers

Exploring Genomics and Microbial Ecology: Analysis of Bidens pilosa L. Genetic Structure and Soil Microbiome Diversity by RAD-Seq and Metabarcoding

Bidens pilosa L., native to South America and commonly used for medicinal purposes, has been understudied at molecular and genomic levels and in its relationship with soil microorganisms. In this study, restriction site-associated DNA markers (RADseq) techniques were implemented to analyze genetic diversity and population structure, and metabarcoding to examine microbial composition in soils from Palmira, Sibundoy, and Bogotá, Colombia. A total of 2,984,123 loci and 3485 single nucleotide polymorphisms (SNPs) were identified, revealing a genetic variation of 12% between populations and 88% within individuals, and distributing the population into three main genetic groups, FST = 0.115 (p < 0.001) and FIT = 0.013 (p > 0.05). In the soil analysis, significant correlations were found between effective cation exchange capacity (ECEC) and apparent density, soil texture, and levels of Mg and Fe, as well as negative correlations between ECEC and Mg, and Mg, Fe, and Ca. Proteobacteria and Ascomycota emerged as the predominant bacterial and fungal phyla, respectively. Analyses of alpha, beta, and multifactorial diversity highlight the influence of ecological and environmental factors on these microbial communities, revealing specific patterns of clustering and association between bacteria and fungi in the studied locations.

Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)

KEY MESSAGE

Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton. Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of Gossypium hirsutum L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (FST) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest FST values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including Transcription factor Vascular Plant One-Zinc Finger 1 (VOZ1) and Protein Photoperiod-Independent Early Flowering 1 (PIE1) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.

Genome-wide diversity evaluation and core germplasm extraction in ex situ conservation: A case of golden Camellia tunghinensis

Whether ex situ populations constructed in the limited nursery resources of botanical gardens can preserve enough genetic diversity of endangered plants in the wild remains uncertain. Here, a case study was conducted with Camellia tunghinensis, which is one of the species with the lowest natural distribution area in the sect. Chrysantha (golden camellia) of the family Theaceae. We investigated the genetic diversity and population structure of 229 samples from wild and ex situ populations using genotyping by sequencing (GBS). Core germplasm was constructed from these samples. The results showed that wild C. tunghinensis exhibited high genetic diversity, with observed heterozygosity of 0.257-0.293 and expected heterozygosity of 0.247-0.262. Compared with wild populations, the genetic diversity of ex situ populations established by transplanting wild seedlings was close to or even higher. However, the genetic diversity of those established by seed or cuttings of a few superior trees was lower. The Admixture analysis revealed that the structure of the ex situ populations derived from seeds and cuttings was relatively simple compared with the ex situ populations derived from transplanted wild seedlings and wild populations. These results suggested that direct transplanting of wild seedlings was more conducive to preserving the genetic diversity of endangered plants in the wild. In addition, wild populations demonstrated a small differentiation (mean F ST = 0.044) among themselves, possibly due to long-term and frequent gene flow between the wild populations. In contrast, moderate differentiation (mean F ST > 0.05) was detected among ex situ populations and between ex situ and wild populations. This may be the combined result of the absence of gene flow pathways and strong selection pressure in various ex situ environments. Finally, 77 core germplasms were extracted from 229, likely representing the genetic diversity of C. tunghinensis. This study provides future strategies for the ex situ conservation and management of the golden camellia species and other rare and endangered plants.

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

The swimming crab, Portunus trituberculatus, is one of the main aquaculture species in Chinese coastal regions due to its palatability and high economic value. To obtain a better understanding of the genetic diversity of P. trituberculatus in the Bohai Sea, the present study used 40 SSR loci to investigate the genetic diversity and population structure of 420 P. trituberculatus individuals collected from seven populations in the Bohai Sea. Genetic parameters revealed a low level of genetic diversity in the cultured population (SI = 1.374, He = 0.687, and PIC = 0.643) in comparison with wild populations (SI ≥ 1.399, He ≥ 0.692, and PIC ≥ 0.651). The genetic differentiation index (Fst) and gene flow (Nm) ranged from 0.001 to 0.060 (mean: 0.022) and 3.917 to 249.750 (mean: 31.289) respectively, showing a low differentiation among the seven populations of P. trituberculatus. Population structure analysis, phylogenetic tree, and principal component analysis (PCA) demonstrated that the seven groups of P. trituberculatus were divided into four subpopulations (K = 4), but the correlation between genetic structure and geographical distribution was not obvious. These results are expected to provide useful information for the fishery management of wild swimming crabs.