Genomic Variation Underlying the Breeding Selection of Quinoa Varieties Longli-4 and CA3-1 in China

Abstract

Quinoa (Chenopodium quinoa) is a well-known climate-resilient crop and has been introduced into multiple marginal lands across the world, including China, to improve food security and/or balanced nutrient supplies. Conventional breeding has been widely applied in the selection and breeding of quinoa varieties in China since 1980s; however, few studies have been implemented on the genetic variances among different varieties developed by diversity breeding objectives. In this study, the phenotypic and genetic differences between two varieties (Longli-4 and CA3-1) from China were systematically analyzed. A total of 407,651 and 2,731,411 single nucleotide polymorphisms (SNPs) and 212,724 and 587,935 small insertion and deletion (INDELs) were detected for Longli-4 and CA3-1, respectively, when compared with the reference genome of PI614886. The SNPs/INDELs were unevenly distributed across each chromosome for both varieties. There were 143,996 SNPs and 83,410 INDELs shared between Longli-4 and CA3-1, accounting for 4% of the total variances. The variation was then screened based on the SNP effects. There were 818 and 73 genes with the variety-specific non-synonymous and stop-gain variation in Longli-4, whereas there were 13,701 and 733 genes in CA3-1. Specifically, 3501 genes with the non-synonymous variation and 74 genes with the stop-gain variation were found in both Longli-4 and CA3-1. These results suggest that convergent selection occurred during the different breeding processes. A set of candidate genes related to agronomic traits and domestication were further selected to detect the genetic divergence in detail in the two varieties. Only one domestication gene was identified having Longli-4-specific stop-gain variation. Twelve candidate genes related to betalain (1), flowering (4), seed size (2), domestication (1), and saponin (4) were identified having CA3-1-specific stop-gain variation. Interestingly, one seed size gene homologous of CKX1 (cytokinin oxidase/dehydrogenase 1) had the stop-gain variation in both varieties. This research will therefore provide guidance for the molecular-assisted breeding in quinoa.

Analysis of Photosynthetic Characteristics and Screening High Light-Efficiency Germplasm in Sugarcane

“…Hybridizing these introduced materials with local varieties increases the chances of genetic diversity in sugarcane, enhancing the population’s adaptability to different environmental conditions [ 66 ] and contributing to broader adaptability and improved growth performance in various regions [ 67 ]. Combining introduced germplasms with local varieties promotes the incorporation of beneficial genetic factors in the offspring, leading to improvements in specific traits [ 68 ], such as enhanced resistance to biotic and abiotic stressors in sugarcane [ 69 , 70 ]. Genetic improvement could achieve superior performance in multiple aspects of new varieties.…”

Phenotypic and genotypic resources for the USDA quinoa (Chenopodium quinoa) genebank accessions

“…Li et al. (2022) reported 16.7% heterozygosity for variety Longli‐4 by using SNPs. Our study confirmed a range of 4.9% and 21.9% and an average heteropoietic of 11.76% across all germplasms.…”

“…By using genome wide markers, we were able to estimate a range Crop Science of 4.9% and 21.9% for heterozygosity among these quinoa accessions. Li et al (2022) reported 16.7% heterozygosity for variety Longli-4 by using SNPs. Our study confirmed a range of 4.9% and 21.9% and an average heteropoietic of 11.76% across all germplasms.…”

Progress in research on the effects of quinoa (Chenopodium quinoa) bioactive compounds and products on intestinal flora

“…Today, C. quinoa is mainly cultivated in South America and Asia, and in China, it is grown primarily in Shanxi and Qinghai provinces, and the northwest of the country. It is noted as a particularly nutrient-rich grain crop and a valuable source of proteins, fat, minerals, vitamins, fiber, and other nutrients, the levels of which tend to be higher than those in more common cultivated grain crops ( 1 , 2 ). Quinoa is considered a whole-grain product containing a rich variety of bioactive substances, including phenols, saponins, and glucans, and can play potentially essential roles in the treatment of different diseases ( 3–5 ), based on the anti-oxidative, anti-cancer, anti-radiation, antibacterial and cholesterol metabolism-regulatory effects of its constituent ( 6 ).…”