Genome-wide association study reveals the genetic basis of amino acids contents variations in Peanut (Arachis hypogaea L.).

Peanut is a significant source of protein for human consumption. One of the primary objectives in peanut breeding is the development of new cultivars with enhanced nutritional values. To further this goal, a genome-wide association study (GWAS) was conducted to analyze seed amino acids contents in 390 diverse peanut accessions collected worldwide, mainly from China, India, and the United States, in 2017 and 2018. These accessions were assessed for their content of 10 different amino acids. Variations in amino acids contents were observed, and arginine (Arg) was found to have the highest average value among all the amino acids quantified. The geographical distribution of the accessions also revealed variations in amino acids contents. High and positive correlation coefficients were observed among the amino acids, suggesting linked metabolic pathways or genetic regulation. A total of 88 single nucleotide polymorphisms (SNPs) spanning various chromosomes were identified, each associated with different amino acids. By using a combination of GWAS, expression anlaysis, and genomic polymorphisim comparisions, the Ahy_A09g041582 (LAC15) gene located on chromrosome A09 was identified as the key candidate which might be involved in plant growth and regulation and may alter amino acids levels. Expression analysis indicated that Ahy_A09g041582 has higher expressions in the shells and seeds than other genes located in the candidate region. This study may help with marker-based breeding of peanuts with higher nutritional value and offers fresh insights into the genetic basis of the amino acids contents of peanuts.

Watermelon domestication was shaped by stepwise selection and regulation of the metabolome.

Although crop domestication has greatly aided human civilization, the sequential domestication and regulation of most quality traits remain poorly understood. Here, we report the stepwise selection and regulation of major fruit quality traits that occurred during watermelon evolution. The levels of fruit cucurbitacins and flavonoids were negatively selected during speciation, whereas sugar and carotenoid contents were positively selected during domestication. Interestingly, fruit malic acid and citric acid showed the opposite selection trends during the improvement. We identified a novel gene cluster (CGC1, cucurbitacin gene cluster on chromosome 1) containing both regulatory and structural genes involved in cucurbitacin biosynthesis, which revealed a cascade of transcriptional regulation operating mechanisms. In the CGC1, an allele caused a single nucleotide change in ClERF1 binding sites (GCC-box) in the promoter of ClBh1, which resulted in reduced expression of ClBh1 and inhibition of cucurbitacin synthesis in cultivated watermelon. Functional analysis revealed that a rare insertion of 244 amino acids, which arose in C. amarus and became fixed in sweet watermelon, in ClOSC (oxidosqualene cyclase) was critical for the negative selection of cucurbitacins during watermelon evolution. This research provides an important resource for metabolomics-assisted breeding in watermelon and for exploring metabolic pathway regulation mechanisms.