Genetic diversity of nutritional quality traits is crucial for potato breeding efforts to develop better varieties for the diverse market demands. In this study, the genetic diversity of 104 potato genotypes was estimated based on nutritional quality traits such as color parameters, total phenolic content, total flavonoid content, 2,2-Diphenyl-1-picrylhydrazyl (DPPH), and 2,2-azino-bis-(3-ethylbezothiazoline-6-sulphonic acid) radical scavenging potential across two environments. The results indicated that environment II, Hangzhou 2020, exhibited higher bioactive compounds and antioxidant properties than environment I, Hangzhou 2019. The colored potato accessions exhibited higher levels of total phenolic content, total flavonoid content, DPPH, and ABTS activities than the white potato accessions, indicating the superiority of the colored to white potato accessions. The genome sequencing identified 1,101,368 high-quality single-nucleotide polymorphisms (SNPs), and 141,656 insertion/deletions (Indels). A population structure analysis revealed that genotypes can be divided into two subpopulations. Genome-wide association studies (GWAS) identified 128 significant SNPs associated with potato’s color, total phenolic content, total flavonoid content, and antioxidant properties. Thus, the study provides new opportunities for strategic breeding and marker-assisted selection of ideal varieties and favorable alleles to enhance bioactive compounds and health-beneficial properties.

The Shanlan landrace rice in Hainan Province, China, is a unique upland rice germplasm that holds significant value as a genetic resource for rice breeding. However, its genetic diversity and its usefulness in rice breeding have not been fully explored. In this study, a total of eighty-four Shanlan rice, three typical japonica rice cultivars, and three typical indica rice cultivars were subjected to resequencing of their genomes. As a result, 11.2 million high-quality single nucleotide polymorphisms (SNPs) and 1.6 million insertion/deletions (InDels) were detected. Population structure analysis showed all the rice accessions could be divided into three main groups, i.e., Geng/japonica 1 (GJ1), GJ2, and Xian/indica (XI). However, the GJ1 group only had seven accessions including three typical japonica cultivars, indicating that most Shanlan landrace rice are different from the modern japonica rice. Principal component analysis (PCA) showed that the first three principal components explained 60.7% of the genetic variation. Wide genetic diversity in starch physicochemical parameters, such as apparent amylose content (AAC), pasting viscosity, texture properties, thermal properties, and retrogradation representing the cooking and eating quality was also revealed among all accessions. The genome-wide association study (GWAS) for these traits was conducted and identified 32 marker trait associations in the entire population. Notably, the well-known gene Waxy (Wx) was identified for AAC, breakdown viscosity, and gumminess of the gel texture, and SSIIa was identified for percentage of retrogradation and peak gelatinization temperature. Upon further analysis of nucleotide diversity in Wx, six different alleles, wx, Wx^a, Wx^b, Wxⁱⁿ, Wx^la/mw, and Wx^lv in Shanlan landrace rice were identified, indicating rich gene resources in Shanlan rice for quality rice breeding. These findings are expected to contribute to the development of new rice with premium quality.

The genotypic diversity and genome-wide association study (GWAS) of potato proteins and amino acid content were investigated in two environments: 98 potato accessions in Environment I and 93 in Environment II. Results revealed that aspartic acid was the most abundant amino acid in environment I and glutamic acid in environment II. The limiting amino acids were cysteine in both environments. The environmental variance accounted for more than 40% of the total variance for all traits except for serine and gamma amino butyric acid (GABA), indicating that potato protein and most amino acids were affected by growing seasons. GWAS identified 78 significant loci associated with potato protein and amino acid contents. The pleiotropic loci, especially those located on chromosomes 6, 9, and 11, provide a strong genetic basis for quality improvement. This study provides genetic insights into potato proteins and amino acid diversity, thereby enhancing molecular breeding for nutritional qualities.

The cooking and eating quality (CEQ) of rice is primarily regulated by the Wx and SSIIa genes. Multiple allelic variations in these genes exist in rice, but the effect of allelic combination of Wx and SSIIa on rice CEQ was less understood. In this study, the Wx and SSIIa genes of 164 rice accessions were sequenced, and the effects of nucleotide variation, both individually and in combination, on physicochemical properties such as apparent amylose content (AAC), gelatinization temperature (GT), pasting viscosities and gel texture were analyzed. Six Wx alleles were identified, with the highest AAC found in the Wx^lv allele and the lowest in the wx allele. No significant difference in AAC for the same genotype harvested from two locations, Hangzhou and Sanya, was observed. Three SSIIa alleles were identified, i.e., G/GC, G/TT, and A/GC. The genotype with the G/GC exhibited significantly higher GT than those with G/TT and A/GC genotypes. However, the GT of the same genotype was higher in Hangzhou than in Sanya, suggesting an environmental effect. Under the same Wx^lv allele background, the gel hardness (HD) of G/TT allele of SSIIa was the highest among all combinations, and significantly higher than that of G/GC. Under the same wx allele background, the peak viscosity (PV), hot paste viscosity (HPV), and cold paste viscosity (CPV) of G/GC were significantly higher than that of G/TT and A/GC. Under the same G/GC allele of SSIIa background, Wx^lv had a slightly lower peak temperature (Tp) and a slightly higher enthalpy of gelatinization (ΔHg) than other allele combinations. Under the same G/TT allele of SSIIa background, Wx^b had a significantly lower onset temperature (To), Tp and conclusion temperature (Tc) than other combinations. This study indicated that variation in the Wx gene primarily affects AAC, viscosity and gel texture, with its interaction with SSIIa influencing GT, while variation in the SSIIa gene primarily affects GT, with its interaction with Wx influencing pasting viscosity.

Shanlan rice, a unique drought-resistant rice germplasm resource in Hainan Province, China, holds significant potential for rice genetic improvement and breeding innovation. However, its genetic diversity and significance in rice breeding remain inadequately explored. This study conducted a comprehensive analysis of phenolic acid profiles and antioxidant properties in the brown rice of 84 Shanlan rice accessions. It was revealed that colored Shanlan rice accessions exhibited significantly higher total phenolic content (249.00–2408.33 mg gallic acid equivalents per 100 g of rice flour (mg GAE/100 g)) and antioxidant capacity (DPPH: 680.39–809.63 micromoles of Trolox equivalent per 100 g (μmol TE/100 g); ABTS: 529.93–1917.77 μmol TE/100 g) compared to white-grained varieties. High-performance liquid chromatography (HPLC) analysis identified eight phenolic acids in the bound fractions, among which the sinapic acid (55.08 μg/g) and vanillic acid (11.72 μg/g) were predominant, accounting for over 60% of total bound phenolic acid content. A genome-wide association study (GWAS) identified 84 significant loci associated with these phenolic-related traits. A major quantitative trait locus (QTL) on chromosome 7 for free phenolic content, total phenolic content, flavonoids, and DPPH activity was co-located at the Rc gene locus, a key regulator of red pericarp pigmentation and proanthocyanidin biosynthesis. Haplotype analysis identified ten haplotypes in Rc, with the haplotype H002 showing the highest antioxidant capacity. Another QTL on chromosome 11 was associated with p-coumaric, vanillic, and sinapic acids, although no significant difference was observed in haplotype analysis. These results highlight Rc as a key genetic factor underlying antioxidant properties in rice, while other loci require further validation. This research provides a foundation for breeding health-benefit, drought-tolerant rice cultivars using Hainan’s unique germplasm.