First Genome of the Brown Alga Undaria pinnatifida: Chromosome-Level Assembly Using PacBio and Hi-C Technologies

Undaria pinnatifida is an important economic brown alga in East Asian countries. However, its genetic and genomic information is very scarce, which hinders further research in this species. A high-density genetic map is a basic tool for fundamental and applied research such as discovery of functional genes and mapping of quantitative trait loci (QTL). In this study the recently developed specific length amplified fragment sequencing (SLAF-seq) technology was employed to construct a high-density genetic linkage map and locate a sex determining locus for U. pinnatifida. A total of 28.06 Gb data including 140.31 M pair-end reads was obtained. After linkage analysis 4626 SLAF markers were mapped onto the genetic map. After adding the sex linked simple sequence repeat (SSR) marker [GenBank:AY738602.1], the final genetic map was 1816.28 cM long, consisting of 30 linkage groups with an average distance of 0.39 cM between adjacent markers. The length of LGs ranged from 20.12 to 106.95 cM. A major sex associated QTL was mapped to LG22 within a window starting at 29.01 cM and ending at 68.81 cM with a total of 68 SLAF markers. The SSR marker and five SLAF markers (Marker6556, 19020, 43089, 60771 and 26359) were identified as tightly sex-linked markers, as indicated by the absence of recombination between them and the sex phenotype. These markers were located at the position of 59.50 cM, which was supposed to be the sex determining region. A high-density genetic linkage map was constructed using SLAF-seq technique and F1 gametophyte population for the first time in the economically important brown alga U. pinnatifida. For the first time, a major sex associated QTL suggesting a sex determining region was mapped to a single LG. This map will facilitate the further fundamental and applied research such as QTL mapping and map-based gene clone in U. pinnatifida and provide a reference for studies in other kelp species.

Undaria pinnatifida is the commercially second most important brown alga in the world. Its global annual yield has been more than two million tonnes since 2012. It is extensively cultivated in East Asia, mainly consumed as food but also used as feed for aquacultural animals and raw materials for extraction of chemicals applicable in pharmaceutics and cosmetics. Cultivar breeding, which is conducted on the basis of characteristics of the life history, plays a pivotal role in seaweed farming industry. The common basic life history shared by kelps determines that their cultivar breeding strategies are similar. Cultivar breeding and cultivation methods of U. pinnatifida have usually been learned or directly transferred from those of Saccharina japonica. However, recent studies have revealed certain peculiarity in the life history of U. pinnatifida. In this article, we review the studies relevant to cultivar breeding in this alga, including the peculiar component of the life history, and the genetics, transcriptomics and genomics tools available, as well as the main cultivar breeding methods. Then we discuss the prospects of cultivar breeding based on our understanding of this kelp and what we can learn from the model brown alga and land crops.