The presence of cadmium (Cd) in rice poses a significant health risk to consumers, highlighting the urgency of breeding rice varieties with low Cd accumulation. To identify genetic resources and potential genes for developing such rice varieties, a comprehensive genome-wide association study (GWAS) was conducted on 158 rice varieties, which tested between 2021 and 2023 in low cadmium accumulation testing framework, to identify candidate genes associated with cadmium content in brown rice. Based on their parental origin and genetic population structure analysis, we categorized these 158 varieties into four subgroups: Luohong, lcd1, intermediate and early indica series. Specifically, the four subgroups of low cadmium varieties were breeded based on OsNramp5 mutants Luohong 3A/4A, lcd1, Lian 1S and Shaoxiang 100, respectively. GWAS analysis identified sixteen loci significantly associated with cadmium content, twelve of which showed consistent associations across multiple environments, these loci were mapped to chromosomes 1, 2, 5, 7, 11, and 12, suggesting their potential for further fine mapping and functional validation. Through gene function annotation analysis, candidate genes related to cadmium content in these loci were identified, including Os05 g0382200, Os07 g0232800 (OsZIP8), Os07 g0232900 (OsHMA3), Os07 g0257200 (OsNramp5), Os07 g0258400 (OsNramp1), Os12 g0512100, Os12 g0512700, and Os12 g0514000. These genes are implicated in the absorption, transport, and accumulation of heavy metals, particularly cadmium. Haplotype analysis of key genes OsZIP8, OsHMA3, OsNramp5, and OsNramp1 identified specific low-cadmium dominant haplotypes. Notably, OsHMA3-Hap2 (GC), OsNramp5-Hap1 (DEL), and OsNramp1-Hap1 (DEL) were associated with Luohong-origin varieties, while OsHMA3-Hap1 (AC), OsNramp5-Hap2 (AA), and OsNramp1-Hap2 (GGG) were linked to lcd1-origin varieties. Overall, this study illustrated the genetic basis for breeding low-cadmium rice varieties and provided candidate loci to develop molecular markers to enhance food safety through reduced heavy metal content.

Background/Objectives: Procambarus clarkii is an important freshwater aquaculture species in China which has the characteristics of rich nutrition and delicious taste. However, the expansion of aquaculture scale, germplasm degradation, and other problems that have become increasingly prominent seriously restrict the sustainable development of the crayfish industry. Genetic improvement is an urgent need for the crayfish aquaculture industry, and selective breeding is an important way to improve the crayfish varieties. Methods: We established full-sibling family populations of the red swamp crayfish and performed whole-genome resequencing of the F3 family-selected red swamp crayfish population and wild red swamp crayfish populations from four regions of Hunan Province (Nanx, Mil, Caish, and Wangc). Results: The results showed that there was a clear separation between the wild population and the family population, and the decline rate was slightly faster in the wild population than that of the family breeding population. There was local gene flow between family populations, as well as gene flow between Mil, Caish, and families. In addition, 52 SNP loci related to body weight traits were identified by genome-wide association analysis, and the candidate gene WIPF1 related to growth was screened out. Conclusions: We established a line selection population of red swamp crayfish and obtained more stable candidate lines. In addition, this study identified Wiskott–Aldrich syndrome protein-interacting protein family member 1 (WIPF1) as a candidate gene related to body weight for the first time. The results provide a theoretical basis for exploring the growth mechanism of P. clarkii and carrying out in-depth genetic improvement.

Ploidy identification is a basic method for determining germplasm resources and for breeding new varieties of oil-seed camellia. In this study, flow cytometry and K-mer analysis were used to identify the ploidy of oil-seed camellia germplasms. To determine the best tissue organ type, lysis time, and dyeing time, evaluation indices such as the presence of a clear main peak, the ease of sampling, and the coefficient of variation were used. A technique was established, and the ploidies of different oil-seed camellia germplasms were identified. The results showed that pollen was the best material and that using a 400 mL PI lysis solution for 10 min lysis, followed by dyeing with a 1600 mL DAPI dyeing solution for 10 min, was the most suitable technique. According to the peak value of the control diploid Camellia azalea, 15 samples were estimated to be diploid, 24 samples were tetraploid, 18 samples were hexaploid, and 13 samples were octoploid. In addition, the K-mer analysis results showed that among the five samples, CK, C051, and C047 were diploid, while C037 and C043 were tetraploid, results that are consistent with the results of the flow cytometry identification. This study is therefore valuable for the polyploid selection and use of different ploidy germplasm resources for the cross breeding of oil-seed camellia.