Origin And Domestication Of Cultivated Barley Revealed By Gene Resequencing And Grain Protein Content

As one of the oldest,most widely distributed,extensively cultivated,and economically important crops,barley production is the fourth largest in the world.High-yield,good quality and multi-resistant are always the major breeding goals of barley genetic improvement.However,gene pools undergoing domestication experienced dramatic changes in genetic polymorphism due to a long-term selection and intensive breeding,and some allelic combinations,especially rare alleles may be lost.Wild barley,Hordeum vulgare ssp.spontaneum,is the progenitor of cultivated barley,Hordeum vulgare ssp.vulgare,which has a broad geographic distribution and ecological adaptation.Natural populations of wild barley have long been recognized as a valuable genetic resource because of its abundant natural variation and genetic diversity.However,The potential to fully exploit genetic variation in the wild progenitors of barley depends,in part,not only on the examination of the genetic structure in wild populations,including determining which portions of the range of wild progenitors have and have not contributed to diversity in the domesticates,but also on the understanding of the genetic basis and genetic background of the current barleys.The origin and domestication of cultivated barley have been widely discussed;however,the debate on these subjects still remains.Here,population-based resequencing and domestication-related traits(grain protein content,GPC)analysis were performed to address barley domestication,to explore genetic differentiation of barley populations on the worldwide scale,and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation.The main findings are as follows:1.The grain protein content(GPC)in 118 cultivated and 93 wild barley accessions ranged from 6.73 to 12.35% with a mean of 9.43%.Overall,wild barley had higher averaged GPC(10.44%)than cultivated barley.Two unique haplotypes(Hap2 and Hap7)might have a significant impact on the GPC.The SNP at position 544 is within the coding region and causes a non-synonymous change in Hap2 and Hap7,which might have an impact on DNA-binding ability of NAM-1 gene,and further affect GPC.2.The current results showed significant genetic differentiation among wild barley populations.The distinct haplotype composition were detected among Tibetan,Central Asian,and Southwest Asian wild barley.Seven NAM-1 haplotypes were population specific,four specific to the Southwest Asian wild population,three specific to the Tibetan wild barley population and no population-specific haplotype was found in wild barley from Central Asian.Moreover,eighteen RPB2 gene haplotypes were wild population specific: 15,2 and 1 were specific to the Southwest Asian,Central Asian and Tibetan wild barley population,respectively.The distinct amplified pattern and sequence variation were detected also.Our phylogenetic analysis and population structure analysis also showed a certain degree of separation among Tibetan,Southwest Asian,and Central Asian wild barleys.3.Tibetan wild germplasms have important contribution to the worldwide cultivated barley gene pools.Genetic variation analyses of NAM-1 gene revealed a high haplotype diversity(Hd = 0.679),per-site nucleotide diversity(? = 0.00090 ± 0.00058),as well as the greatest nucleotide diversity(? = 0.00103)in Tibetan wild barley population.The haplotype analysis showed that the worldwide cultivars shared the same haplotypes with the wild barley from the Tibet.This was particularly evident for the NAM-1 haplotype Hap7,which was observed in 37.4% barley accessions,and also widely distributed in all cultivated population at a frequency of 0.475 to 0.875.Also noticeable was the RPB2 haplotype-Hap2,which occurs in 32.5% barleys,and also frequently in all cultivated barley populations ranged from 0.361 to 0.778.Sequence comparisons,phylogenetic and population structure analyses also revealed a close relationship between worldwide domesticated barley and the Tibetan wild barley.Our data confirmed that Tibetan Plateau is one of the centers of domestication of cultivated barley.4.Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau,supporting polyphyletic origin of cultivated barley.We suggested that the multiple domestications coupled with widespread introgression events contributed to the modern cultivated barley gene pool.The haplotypes analysis showed a genetic exchange occurred between Eastern and Western barley,it may be assumed that Central Asia is the sole route for barley migration between the Near East and the Qinghai-Tibetan Plateau.A long period of gene flow may have led to subsequent transfer of introgressed haplotypes to cultivars in other regions due to human activities such as germplasm exchange,introduction and hybridization.5.Different wild and cultivated barley showed different domestication traces and artificial selection effects.We confirmed that most alleles in wild types have been lost in the domesticated forms.In our studies,a total of 10 distinct NAM-1 haplotypes were discovered,only 3 haplotypes were detected in the diverse set of 120 domesticated barleys from across the world.Similarly,among the 21 haplotypes of RPB2 sequence found in all barley accessions,only eight were present in the domesticated lines,while more haplotypes occurred in wild barley accessions.Genetic diversity was also significantly reduced in cultivated barley.As expected in RPB2,about 18.2% nucleotide diversity,13.5% haplotype diversity and two-fold of per-site nucleotide diversity reduction in cultivated barley.Genetic bottleneck due to domestication and breeding is the major determinant of polymorphism loss in the domesticated lines.Moreover,our data showed divergent domestication pressures acting on geographically discontinuous barley populations.Our results not only provide important insight into the domestication and evolution of cultivated barley,but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations,thus further facilitating the effective use of the wild barley germplasm.