Genome-wide patterns of large-size presence/ absence variants in sorghum

• Published in: Journal of integrative plant biology Vol. 56; no. 1; pp. 24 - 37
• Main Authors: Zhang, Li-Min, Luo, Hong, Liu, Zhi-Quan, Zhao, Yi, Luo, Jing-Chu, Hao, Dong-Yun, Jing, Hai-Chun
• Format: Journal Article
• Language: English
• Published: China (Republic : 1949- ) Blackwell Publishing Ltd 2014; The Key Laboratory of Plant Resources, Institute of Botany, The Chinese Academy of Sciences, Beijing 100093, China%college of Life Sciences, Peking University, Beijing 100871, China%Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun 130012, China
• Subjects: Breeding; Chromosomes, Plant - genetics; Crosses, Genetic; DNA Transposable Elements - genetics; Gene Ontology; Genes, Plant - genetics; genetic diversity; Genetic Variation; Genome Size - genetics; Genome, Plant - genetics; genomics; Inbreeding; Inheritance Patterns - genetics; Molecular Sequence Annotation; presence/absence variants; Retroelements - genetics; Sequence Analysis, DNA; Sorghum - genetics; Sorghum bicolour; 全基因组; 变种; 基因组变异; 大尺寸; 植物基因组; 测序工作; 结构变异; 高粱属; presence/absence variants; genetic diversity; Sorghum bicolour; genomics; Breeding
• ISSN: 1672-9072; 1744-7909
• DOI: 10.1111/jipb.12121

The presence/absence variants （PAVs） are a major source of genome structural variation and have profound effects on phenotypic and genomic variation in animals and humans. However, little is understood about PAVs in plant genomes. Our previous resequencing effort on three sorghum （Sorghum bicolour L.） genomes, each 12？ coverage, uncovered 5 364 PAVs. Here, we report a detailed characterization of 51 large-size （＆gt;30 kb） PAVs. These PAVs spanned a total size of 2.92 Mb of the sorghum genome containing 202 known and predicted genes, including 38 genes annotated to encode celldeath and stress response genes. The PAVs varied considerably for repeat sequences and mobile elements with DNA trans-posons as the major components. The frequency and distribution of these PAVs differed substantial y across 96＆amp;nbsp;sorghum inbred lines, and the low-and high frequency PAVs differed in their gene categories. This report shed new light on the occurrence and diversity of PAVs in sorghum genomes. Our research exemplifies a new perspective to explore genome structural variation for genetic improvement in plant breeding.