S11-1

Haplotype-resolved genome assembly provides insights into evolutionary history of the tea plant Camellia sinensis

Xingtan Zhang¹

¹Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

Tea is an important global beverage crop and largely clonally propagated. Despite previous studies on the species, its genetic and evolutionary history deserves further research. Here, we present a haplotype-resolved assembly of an Oolong tea cultivar TGY. Analysis of allele-specific expression suggest a potential mechanism in response to mutation load during long-term clonal propagation. Population genomic analysis using 190 Camellia accessions uncovered independent evolutionary histories and parallel domestication in two widely cultivated varieties, var. sinensis and assamica. It also revealed extensive intra- and inter-specific introgressions contributing to genetic diversity in modern cultivars. Strong signatures of selection were associated with biosynthetic and metabolic pathways that contribute to the flavor characteristics as well as genes likely involved in Green Revolution in tea industry. Our results offer genetic and molecular insights into the evolutionary history and provide genomic resources to further facilitate gene editing to enhance desirable traits in the tea crops.

S11-2

The domestication history of cultivated lettuce revealed by resequencing of 445 Lactuca accessions

Tong Wei¹, Rob van Treuren², Xin Liu¹, Huan Liu¹

¹State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
²Centre for Genetic Resources, the Netherlands, Wageningen, the Netherlands

Cultivated lettuce (Lactuca sativa) is an important vegetable crop and widely consumed as salad greens worldwide. Despite the popularity in urban lifestyle, its domestication history remains to be elucidated. In this study, we sequenced 445 Lactuca accessions, including major crop types and wild relative species, and produced a wealth of sequence variations based on the lettuce reference genome. In-depth analyses revealed that modern lettuce was first domesticated near the Caucasus, close to the Fertile Crescent where major crops, like wheat and barley, were domesticated. Our study provides not only genomic resources for plant breeding but also the genetic mechanisms underlying lettuce domestication.

S11-3

Genomic insight into the early flowering trait of the model rice cultivar Kitaake

Guotian Li¹, Qiping Sun¹, Pamela C Ronald¹

¹Huazhong Agricultural University
²University of California,Davis

Agronomic traits of domesticated crops have been extensively selected to adapt to the local agricultural systems. Flowering time is a key trait that largely determines the geographic distribution of a crop and is therefore carefully selected by human. Kitaake is a very early flowering rice cultivar, originated from Hokkaido, Japan, one of the world’s northern-limits of rice cultivation. To gain genetic insight into the early flowering trait of Kitaake, we sequenced and assembled the Kitaake genome at a high-quality level with a scaffold N50 of 30.3 Mb. We compared the Kitaake genome with worldwide rice accessions including multiple wild rice species and found that more than 10 genes regulating flowering time might have been artificially selected in Kitaake to adapt the local short growing season. To genetically analyze the candidate genes, we established a segregating population and confirmed that GHD7 and OsPRR37 are the two major genes contributing to the early flowering trait of Kitaake. Interestingly, we also identified several minor alleles controlling flowering time. To further shorten the life cycle of Kitaake, we took advantage of a whole-genome sequenced mutagenized population and artificially selected multiple lines that flower earlier than Kitaake. We cloned these genes and one of them is a novel gene (OWD2), which fine tunes the flowering time. We stacked these alleles together in Kitaake and achieved a line that enables researchers to grow six generations a year in a controlled environment, demonstrating the possible artificial selection in flowering time in rice.

S11-4

Diversity and Genetics of Important Traits in Eggplant

Prashant Kaushik¹

¹Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022 Valencia, Spain

Eggplant´s wild species remain underutilized in eggplant breeding programs. The detailed phenotypic and biochemical characterization, and the identification of the genetics of these crucial traits of the wild species and their hybrids may help identify and research valuable species and attributes. Therefore, here characterization of 6 cultivated eggplant accessions, 21 accessions of wild species, and 45 interspecific eggplant hybrids were studied for morphological and biochemical variation and also for the extent of heterosis. Further, the genetics of some important traits was dissected with Line by Tester matting design. A great deal of consistent difference was found between the cultivated, wild, and interspecific hybrid groups. Several accessions of wild populations have greater variation in morphology than in interspecific hybrids, but fruit shape traits have the most significant variation. Similarly, a high degree of variation was determined for the fruit biochemical traits, especially chlorogenic acid being highest in the wild species. Much species diversity was found, helping in identifying species with tremendous potential. Whereas, genetically specific combining ability (SCA) component had higher values than the general combining ability (GCA) component. For the majority of traits, the testers were more significant than the cultivated varieties. This work was crucial in identifying crop domestication and evolution of eggplant.

S11-5

The Genetic History of Apple Domestication

Xuepeng Sun¹

¹Zhejiang A&F University
²Boyce Thompson Institute, Cornell University

Domestication of apple was mainly driven by interspecific hybridization. Here, we report the haplotype-resolved genomes of cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes with hundreds of them been selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.

S11-6

Reference genome of spinach and resequencing of 305 Spinacia accessions provide insights into molecular basis of agronomic traits

Chen Jiao¹

¹Zhejiang University

Spinach is an important nutritious leafy vegetable belonging to the family Chenopodiaceae. We assembled the chromosome-scale reference genome of spinach (Spinacia oleracea, 2n=12) with more than 98% of the sequences anchored and ordered on the six chromosomes. Reconstruction of ancestral Chenopodiaceae karyotype (ACK) suggested a substantial genome rearrangement in spinach after divergence from ancestral Chenopodiaceae, which coincided with the high level of repeat content in the spinach genome. Transcriptomic and genomic sequencing of a large collection of cultivated and wild spinach accessions suggested that S. turkestanica is likely the direct progenitor of cultivated spinach and the domestication has experienced a weak bottleneck. Twenty agronomically important traits in spinach were investigated using a high-density SNP data set, which yielded significantly associated regions and gene candidates for each trait. We also identified hundreds of selective sweeps in the spinach genome, some of which are associated with important agronomic traits (e.g. leaf phenotype, bolting, and flowering), demonstrating the role of artificial selection on shaping the phenotypic evolution of cultivated spinach during domestication. In conclusion, this study provides not only the novel insights into the spinach evolution and domestication but also valuable resources for facilitating spinach breeding in the future.