Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China

Abstract

The domestication process of cultivated barley in China remains under debate because of the controversial origins of barley. Here, we analyzed transcriptomic and non-targeted metabolic data from 29 accessions together with public resequencing data from 124 accessions to explore the domestication process of cultivated barley in China (Cb-C). These analyses revealed that both Cb-C and Tibetan wild barley (Wb-T) were the descendants of wild barley from the Near East Fertile Crescent (Wb-NE), yielding little support for a local origin of Wb-T. Wb-T was more likely an intermediate in the domestication process from Wb-NE to Cb-C. Wb-T contributed more genetically to Cb-C than Wb-NE, and was domesticated into Cb-C about 3300 years ago. These results together seem to support that Wb-T may be a feralized or hybrid form of cultivated barley from the Near East Fertile Crescent or central Asia. Additionally, the metabolite analysis revealed divergent metabolites of alkaloids and phenylpropanoids and these metabolites were specifically targeted for selection in the evolutionary stages from Wb-NE to Wb-T and from Wb-T to Cb-C. The key missense SNPs in the genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be responsible for the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Our findings allow for a better understanding of the domestication process of cultivated barley in China.

Population Genetic Analysis of a Bread Wheat Panel from Northern and Huang-Huai Agro-Ecological Regions in China

“…The software Plink version 1.90b6.18 was employed to calculate the minor allele frequency (MAF) at each locus of each population by using the ped and map files as input files with the parameter "--freq --noweb --missing --withing pop.cov", where "pop.cov" is the grouped file of samples from the three geographical populations. At each population, the polymorphism information content (PIC) and the expected heterozygosity (H exp ) at each locus were calculated by using the following formulas reported by Zhou et al [39]:…”

“…The analysis was carried out in four steps. First, one gene pool for each of the five bread wheat groups (Hebei, Henan, Shandong, Landrace1, and Landrace2) was constructed based on the previously reported method [39,41,42]. Briefly, if a locus had two or more variants, the minority variants were treated as errors in a group.…”

“…Environmental factors, including altitude, frost-free days, annual sunlight, temperature, precipitation, and soil type, may have driven the regional/local genetic divergence and altered the genetic diversity of landrace wheat, wild emmer wheat, and wild barley [10,39,46,47]. Artificial selection has been confirmed to be a major force shaping the population structure of wheat germplasm [3,14,48,49].…”

“…In barley, Dai et al [42] indicated that wild barley of the Fertile Crescent contributes more genomic regions to the genome of cultivated barley in chromosomes 1H, 2H, and 3H, while wild barley of Tibet contributes more genomic regions in chromosomes 4H, 5H, 6H, and 7H. In addition, Zhou et al [39] reported that wild barley of Tibet genetically contributes more to cultivated barley of China than wild barley from the Fertile Crescent. Wheat landraces are highly valuable genetic and breeding resources.…”

Bacterial Community Structure in Rhizosphere of Barley at Maturity Stage

“…Barley has more than 5000 years of cultivation history in China [7]. It is mainly used as feed and beer industrial raw materials, and it is also the most important rotation crop and functional health food for Tibetan compatriots [8].…”