Studies On Domestication And Spread Of Broomcorn Millet Based On Reduced Representation Sequencing

Broomcorn millet(Panicum miliaceum L.),one of the most ancient crops in the world,is widely cultivated in the semiarid regions of Asia,Europe and America.Weedy broomcorn millet(Panicum ruderale(Kitag.)Chang comb.Nov.or Panicum miliaceum subsp.ruderale(Kitag)Tzvel),the companion weed of cultivated broomcorn millet,is also widely distributed in various cultivated areas of broomcorn millet.In this study,we developed a large number of single nucleotide polymorphism(SNP)sites by using Specific-Locus Amplified Fragment Sequencing(SLAF-seq)technology in Reduced representation genome sequencing(RRGS).The population genetic analysis of weedy broomcorn millet in China and cultivated broomcorn millet in Eurasia was carried out to reveal the genetic relationship between weedy and cultivated broomcorn millet,and to explore the domestication and spread of cultivated broomcorn millet.The main results of this study are as follows:(1)Results of Admixture analysis show that all weedy broomcorn millet and cultivated broomcorn millet are classified into Group I,Group II-A,Group II-B,Group III-A,Group III-B when k=5.Samples of Group I are all composed of weedy broomcorn millet,samples in Group II-A are widely distributed in northern China,and it is the main type of Chinese cultivated broomcorn millet.Samples in Group II-B are mainly distributed in northern China and North Korea,South Korea and Japan.Group III-A is composed of cultivated broomcorn millets distributed in Mongolia,Russia,Kazakhstan and their surrounding areas.Cultivated broomcorn millets in Group III-B are widely distributed in South Asia,Central Asia,West Asia and Europe,while their distribution in China is limited in Xinjiang.(2)Results of phylogenetic analysis show that Groups can basically be separated from each other in the phylogenetic tree,which is consistent with the results of Admixture analysis.All the weedy broomcorn millets of Group I clustered together,and the genetic relationship between weedy samples of Group I and some cultivated samples of Group II-A from the Loess Plateau and Northeast China is relatively close.In addition,among the samples of Group II-B,four samples from Japan,North Korea and South Korea have the closest genetic relationship,and the genetic relationship between Group III-B sample from India and Group III-B samples TAJ1,AFG1,and AFG2 from Tajikistan and Afghanistan is relatively close.Besides,the genetic relationship between Group III samples and some samples in Group II-A subgroup(most of them come from Northeast China)is the closest;(3)Results of principal component analysis(PCA)show that weedy broomcorn millet(Group I)and cultivated broomcorn millet(Group II,Group III)are clearly separated on the first principal component(PC1).Cultivated broomcorn millet of Group II and Group III are well separated on the second principal component(PC2).Samples of Group II are distributed in eastern Eurasia,while samples of Group III are widely distributed in central,western and north regions of Eurasia.Cultivated broomcorn millet samples from Japan,North Korea and Sorth Korea show the closest genetic distance,which was relatively far away from other samples of this subgroup.(4)The nucleotide diversity(π),observed heterozygosity(H_O)and expected heterozygosity(H_E)of weedy broomcorn millet populations are higher than that of cultivated broomcorn millet populations.The genetic differentiation between Group I and Group II/Group III is obvious,while the genetic differentiation between Group II and Group III is not obvious.(5)Selective sweeps analysis identified 933 selective sweeps including 2424 candidate genes.The genes entries annotated in selective sweeps were assigned to Gene Ontology(GO)terms,which are summarized into three principal categories:biological process(20),cellular component(11),molecular function(11).In summary,we concluded that:(1)Plenty of wild type and some feral type of individuals are included in Weedy broomcorn millet.The wild type broomcorn millets may contain the ancestral inherited types of cultivated broomcorn millets.Obvious genetic differentiation has occurred between weedy and cultivated broomcorn millet populations due to the effect of domestication bottlenecks and artificial selection.(2)The weedy samples of Group I may be the wild type,while the weedy sample WSX26attributed into Group II is probably to be the endoferal type formed by escaped from cultivars,and weedy sample WSX 25 which is the admixture with large proportion of gene pools in Group I and Group II may be that exoferal type formed by hybridization between wild types and cultivars.(3)Supporting the viewpoint that the Loess Plateau in China and Northeast China are possible domestication areas of cultivated broomcorn millet.Group III-A may derived from the Eurasian steppe or Northeast China,and Group III-B may formed in Xinjiang or somewhere on its westward route.(4)Cultivated broomcorn millet of Group II spread throughout the northern China after domestication.A few of them spread westward through Gansu Hexi Corridor to Xinjiang,cultivated broomcorn millet of Group II-A spread westward through Central Asia to Central Europe via Oasis Route,while cultivated broomcorn millet of Group II-B spread to Altai in northern Xinjiang.(5)The cultivated broomcorn millets of Group III-A spread westward to the north of the Caspian Sea and the Black Sea via“Steppe Route”,which through the Mongolian Plateau,Kazakh hills,Siberian plains and Eastern European plains.The cultivated broomcorn millets of Group III-B spread to the south of the Caspian Sea and the Black Sea through Pamir Plateau,Central Asia,Western Asia along the“Oasis Route”.(6)The cultivated broomcorn millets in India belong to Group II-A and Group III-B,the former may be introduced from Northern China through the"South Asian Mountain Corridor",and the latter may be introduced from Tajikistanan or Afghan during its westward spread via“Oasis Route”.(7)The cultivated broomcorn millets from Japan,South Korea and North Korea are attributed to Group II-B,and they may introduced from Northeast China,Shandong or Liaodong Peninsula,or the Far East of Russia.In this study,several issues such as genetic relationship between weedy broomcorn millet and cultivated broomcorn millet,and spread routes of cultivated broomcorn millet were deeply explored.These results will provide valuable molecular genetic information for the study of domestication and spread routes of cultivated broomcorn millet.It also provides an important experimental basis for the protection of genetic diversity,development of wild resources and introduction and domestication of broomcorn millet.