Abstract
Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America–Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.
Highlights
Sunflower (Helianthus annuus spp. macrocarpus) is one of the most important oilseed crops, with a global production value estimated at USD 20 billion per year (FAO 2016)
Data generation: The pre-breeding collection of Instituto Nacional de Tecnología Agropecuaria (INTA), composed of 135 sunflower inbred lines preserved at the Active Germplasm Bank of INTA Manfredi (AGB-IM), was genotyped using a double digest restriction-site associated DNA sequencing protocol adapted from Peterson et al [16]
The analysis of molecular variance (AMOVA) using 11,834 Single nucleotide polymorphisms (SNPs) revealed significant genetic differentiation of populations, with variation among breeding collections, representing 4.58% of the total genetic variance (p < 0.01, 999 permutations)
Summary
Sunflower (Helianthus annuus spp. macrocarpus) is one of the most important oilseed crops, with a global production value estimated at USD 20 billion per year (FAO 2016). 4000 years ago, but it became an oil crop only when it reached Russia late in the XVIIIth century. The foundational efforts of Pustovoit at VNIIMK to develop high yielding, open-pollinated varieties with high oil content are considered the main genetic base of modern sunflower breeding [1]. Helianthus petiolaris and cultivated sunflower [2] and fertility restoration genes [3] at the United States. Argentina has a long tradition in sunflower breeding. Since 1931, and by exploiting the diversity of a broad range of foreign genetic resources in combination with introgressions of wild Helianthus species Since 1931, and by exploiting the diversity of a broad range of foreign genetic resources in combination with introgressions of wild Helianthus species (e.g., H. annuus, H. argophyllus, and H. debilis ssp. cucumerifolius), the Instituto Nacional de Tecnología Agropecuaria (INTA) has pioneered sunflower breeding and has become one of the most prolific sunflower breeders in the country [4,5,6]
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