Copy number variation of B1 controls awn length in wheat

Wheat awns contribute to photosynthesis and grain production.In this study,an F2population and F2:3families from a cross between the awned line 7D12 and the Chinese awnless variety Shiyou 20(SY20)were used to identify loci associated with awn length.Bulked-segregant RNA sequencing and linkage mapping identified a single dominant locus in a 0.3 cM interval on chromosome 5AL.Five genes were in the interval,including the recently cloned awn inhibitor B1.Although a single copy of the B1 gene was detected in 7D12,SY20 carried five copies of the gene.Increased copy number of B1 in SY20enhanced gene expression.Based on sequence variation among the promoter regions of five B1 gene copies in SY20,two dominant markers were developed and found to cosegregate with B1 in a population of 931 wheat accessions.All 77 awnless accessions harbored sequence variations in the B1 promoter regions similar to those of SY20 and thus carried multiple copies of the gene,whereas 15 randomly selected awned wheats carried only one copy.These results suggest that an increase in copy number of the B1 gene is associated with inhibition of awn length.

A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis

Garlic,an economically important vegetable,spice,and medicinal crop,produces highly enlarged bulbs and unique organosulfur compounds.Here,we report a chromosome-level genome assembly for garlic,with a total size of approximately 16.24 Gb,as well as the annotation of 57561 predicted protein-coding genes,making garlic the first Allium species with a sequenced genome.Analysis of this garlic genome assembly reveals a recent burst of transposable elements,explaining the substantial expansion of the garlic genome.We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans,and provided new insights into the biosynthesis of these two compounds.Furthermore,a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs.The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.

Genome-wide signatures of the geographic expansion and breeding of soybean

Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.

Genome-wide analysis reveals selection for Chinese Rongchang pigs

Livestock have undergone domestication and consequently strong selective pressure on genes or genomic regions that control desirable traits. To identify selection signatures in the genome of Chinese Rongchang pigs, we generated a total of about 170 Gb of DNA sequence data with about 6.4-fold coverage for each of six female individuals. By combining these data with the publically available genome data of 10 Asian wild boars,we identified 449 protein-coding genes with selection signatures in Rongchang pigs, which are mainly involved in growth and hormone binding, nervous system development, and drug metabolism. The accelerated evolution of these genes may contribute to the dramatic phenotypic differences between Rongchang pigs and Chinese wild boars. This study illustrated how domestication and subsequent artificial selection have shaped patterns of genetic variation in Rongchang pigs and provides valuable genetic resources that can enhance the use of pigs in agricultural production and biomedical studies.

Genomic analysis of Tibetan ground tits identifies molecular adaptations associated with cooperative breeding

Cooperative breeding is a sophisticated altruistic social behavior that helps social animals to adapt to harsh environments.The Tibetan ground tit,Pseudopodoces humilis,is a high-altitude bird endemic to the Tibetan plateau.Recently,it has become an exciting system for studying the evolution of facultative cooperative breeding.To test for molecular adaptations associated with cooperative breeding,we resequenced the whole genome of ground tits from 6 wild populations that display remarkable variation in the frequency of cooperative breeding.Population structure analyses showed that the 6 populations were divided into 4 lineages,which is congruent with the major geographical distribution of the sampling sites.Using genome-wide selective sweep analysis,we identified putative positively selected genes(PSGs)in groups of tits that displayed high and low cooperative breeding rates.The total number of PSGs varied from 146 to 722 in high cooperative breeding rate populations,and from 272 to 752 in low cooperative breeding rate populations.Functional enrichment analysis of these PSGs identified several significantly enriched ontologies related to oxytocin signaling,estrogen signaling,and insulin secretion.PSGs involved in these functional ontologies suggest that molecular adaptations in hormonal regulation may have played important roles in shaping the evolution of cooperative breeding in the ground tit.Taken together,our study provides candidate genes and functional ontologies involved in molecular adaptations associated with cooperative breeding in Tibetan ground tits,and calls for a better understanding of the genetic roles in the evolution of cooperative breeding.

Snapshot of Structural Variations in the Tibetan Wild Boar Genome at Single-Nucleotide Resolution

Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation （Alkan et al., 2011; Bickhart and Liu, 2014）. With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps （Li et al., 2011）. Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies （Baker, 2012; Wang et al., 2012;