| The rhizome is an important organ through which many perennial plants are able to propagate vegetatively,and it is also a key organ for plants to adapt to different environment.Over the past 10,000 years,humans have domesticated perennial wild species into annual cultivars,which display increased yields and improved quality.As a result,they show weakened ecological adaptations.The main reason for this phenomenon is that the rhizome,which is an important organ for maintaining plant perenniality,was"lost" during the domestication.Exploring the genetic mechanism of rhizomes adaptation from the perspective of geneticscan help us understand how plants can maintain their environmental adaptation through rhizome-mediated asexual reproduction.Oryza longistaminata is emerging as an ideal specie for studying the genetic mechanism of environmental adaptation of plants’ rhizomes.O.longistaminata originated from West Africa,andit has the same AA genome as cultivated rice(O.sativa),featuring a well-developed rhizome trait to achieve perenniality;therefore,the rhizome of O.longistaminata is suitable for studying the environmental strategies of many perennial species.In this study,following our previous genetic studies of rhizome in O.longistaminata,we constructed an F2 population from a cross between O.longistaminata as the male and the O.sativa as the female cultivar RD23,consisting of 818 individuals.At the same time,a population of 133 single recombinant inbred lines(RILs)was constructed.We evaluated the phenotypic variation and genotypic polymorphism of the rhizome traits in these populations,and finally constructed a genetic network for the regulation of rhizome.Collectively,we revealed the genetic mechanism for the environmental adaptation of rhizome in perennial plants.Major research items are following:(1)Phenotypic evaluation of individuals in F2(RD23/O.longistaminata)population and RILs population.We planted all the F2 plants,their parents(RD23,O.longistaminata)and F1 in the field.At the time of RD23 was heading,all the plants were dug out,and the underground parts of each plant included parents,F1,818 F2 and 133 RIL were washed free of soil for phenotypic evaluation.Each plant was first evaluated for the presence or absence of rhizomes.For individuals with rhizomes,rhizomes-related quantitative traits were measured,including primary rhizome number(RN)Cumulative length of primary branches(RLsum),average length of primary branches(RLmean),maximum length of primary branches(RLmax),number of secondary branches(RB2)Number of third branches(RB3)and number of fouth branches(RB4).(2)Construction of a genetic linkage map of O.longistaminata.The whole genome of the above 821 individuals sequenced by ddRAD-seq(double digestion restriction-site associated DNA sequencing)and obtained SNPs(Single nucleotide polymorphisms)at the whole genome level of each individual,and a genetic linkage map was constructed based on these SNPs.(3)Genetic mechanism of environmental adaptability of rhizome in O.longistaminata.We analyzed the genetic loci and their genetic effects that controlling rhizome based on the phenotypic diversity and genetic diversity in F2 population,and constructed a genetic network for the presence of rhizome in O.longistaminata to analyze the genetic mechanism of environmental adaptation.The results of the study are as follows:(1)Abundant phenotypic variation in rhizome.The phenotypic variation of rhizome of O.longistaminata was abundant.There were 818 plants in F2 population,233 had no rhizome and 585 had rhizome.Of 818 individuals in F2 population,233 had no rhizome and 585 had rhizome.Among the 585 plants with rhizome and rhizome related traits showed abundant variation,and the most rhizome branch number(RN)was 43,with an average of 6.55.The greatest variation was found in RLsum,which was 614 cm with an average length of 53.81 cm;RLmax reached 44 cm with an average length of 11.25 cm;the largest number of second branches(RB2)was 66 with an average of 6.96,but there were also some individuals without RB2.The largest number of the RB3 was 45,with an average of 2.95;RB4 was only 10,with an average of 0.33.Except for the RLmean,which was normally distributed,all other traits were skewed,it fully indicates that the rich phenotypic variation of rhizome in O.longistaminata is responsible for its adaptation to different ecological environments.(2)Thirteen genes controlling rhizome presence(Rhz)in O.longistaminata were identified.The genetic map was constructed based on 1487 SNP markers spanning 1469.27 cM and covering all 12 chromosomes.The average distance between makers was 0.99 cM.It was found that 13 major genetic loci controlling rhizome presence:Rhz-1,Rhz-2,Rhz-3-1,Rhz-3-2,Rhz-4-1,Rhz-5,Rhz-6,Rhz-7,Rhz-8,Rhz-9,Rhz-10,Rhz-11,Rhz-12,which were distributed on 12 chromosomes.The Rhz-4-1 on chromosome 4 was the most effective(χ2=119.16),followed by Rhz-3-1(χ2=46.06)on chromosome 3.In addition to these 13 genetic loci,micro effect loci related to rhizome presence were also found on chromosomes 4,10 and 12:Rhz-4-2(mk1100),Rhz-10-2(mk117)and Rhz-12-2(mk768).The results showed that the rhizome presence was controlled by multiple genes,which may be the genetic basic why plants mainly adapt to the environment.(3)A large number of quantitative trait loci(QTLs)were found to control the development traits of rhizome in O.longistaminata.QTL analysis based on rhizome development in F2 population showed that there were 12,13,6,5,11,12 and 9 QTLs controlling RN,RLsum,RLmean,RLmax,RB2,RB3 and RB4,respectively.These QTLs were mainly additive effects,and the synergistic alleles came from O.longistaminata.The results showed that the genetic model of rhizome related traits is very complex,which is also the genetic basis of rhizome in O.longistaminata with environmental adaptability.(4)We found that complex genetic networks were controlling the development of rhizomes in O.longistaminata.The genetic network of rhizome development of O.longistaminata was constructed by detecting the relationship between rhizome genetic loci.In the comprehensive network of rhizome development,its involved 58 Functional Genetic Units(FGU),which were located on 12 chromosomes,FGU refered to a pair of genes located at the same level and functionally interdependent in the determined signal pathway.These 58 FGUs included 62 pairs of hierarchical QTLs and 104 pairs of E-QTLs.Based on the functional relationship of them,7 genetic networks of rhizome related traits of O.longistaminata were constructed respectively.Moreover,a overview network was constructed,the network included three sub networks that control the presence of rhizome(Network-RHZ),the number and length of rhizome(Network-RN/L),and the branching of rhizome(Network-RB).Network RHZ and network RN/L were linked by qRHI-2,network-RHZ and network-RB were linked by qRHI-5.According to the function and corresponding characteristics of key nodes in genetic network,Rhz-3-1,Rhz-4-1,qRHI-2 and qRHI-5 were the key loci for rhizome development.The corresponding STS markers were developed for the InDel sequences of these four key genetic loci,used RILs population to develop STS markers of Rhz-3-1,Rhz-4-1,qRHI-2 and qRHI-5 for functional verification,the results showed that in the RILs population with rhizome-free,there was no individual could detect the key genetic loci containing more than two O.longistaminata genotypes,and no individual with both qRHI-2 and qRHI-5 of O.longistaminata genotype.The results showed that no genetic locus can independently control the rhizome traits,qRHI-2 and qRHI-5 are likely both needed for rhizome formation.In conclusion,the phenotype and genotype of O.longistaminata rhizomes are highly variable.The rhizome presence is affected by multiple genes,which constitute a complex genetic network to control the development of rhizome.This complex genetic mechanism is one of the reasons for perennial plants to adapt to the environment,and the research results provide genetic theory and reference for the protection and utilization of perennial plants. |
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