RFLP analysis of the progeny from Oryza alta Swallen x Oryza sativa L

Genome-wide and pan-genomic analysis reveals rich variants of NBS-LRR genes in a newly developed wild rice line from Oryza alta Swallen

Introduction

Oryza alta Swallen is an allotetraploid perennial wild rice and contains CCDD genome, which may harbor favorable genes for the enrichment of genetic resource.

Methods

A new wild rice line, Huaye 5, was developed from Oryza alta Swallen in our lab. Whole genome re-sequencing and pan-genomic analysis were employed to analyze its genomic variations and novel genes.

Results and Discussion

More than ten million genomic variations were detected when compared with Asian cultivar. Among the variational genes, 724, 197 and 710 genes coded protein kinase, synthetase and transcription factor, respectively. A total of 353, 131 and 135 variational genes were associated with morphological trait, physiological trait, resistance or tolerance, respectively. A total of 62 were NBS-LRR genes were detected, in which 11 NBS-LRR genes expressed in sheath and mature stem, and 26 expressed in young and mature roots expressed. The pan-genome sequences of wild rice species with CCDD genome were constructed by integrating 8 Oryza alta (OA), 2 Oryza grandiglumis (OG) and 18 Oryza latifolia (OL) accessions. A total of 28 non-reference NBS-LRR genes were revealed, and 7 of which were mainly expressed in mature roots. This research demonstrated rich DNA variation in the Oryza alta Swallen that may provide a new germplasm for rice resistance breeding.

Agrobacterium-Mediated High-Efficiency Genetic Transformation and Genome Editing of Chaling Common Wild Rice (Oryza rufipogon Griff.) Using Scutellum Tissue of Embryos in Mature Seeds

Genetic transformation is an important strategy for revealing gene function, and it is used extensively in both functional genomics study and molecular breeding of rice. Demand for its application in wild Oryza species is rising for their extensive genetic diversity. However, genetic transformation of wild Oryza accessions with AA genome using calli induced from scutellum tissue of embryos in mature seeds has not been successfully established. In the present study, we used Chaling common wild rice (CLCWR) (Oryza rufipogon Griff.) with AA genome to successfully establish an Agrobacterium-mediated genetic transformation system based on scutellum tissue of embryos in mature seeds. The calli from embryos in mature seeds of CLCWR were easy to be induced and regenerated. The callus induction rate and texture were optimum under 2.5 mg/L 2,4-D. The optimal hormone combination used for regeneration was 2 mg/L ZT + 0.1 mg/L NAA. Studies on genetic transformation and genome editing showed that the transformation efficiency was 87-94%, the efficiency of single genome editing and multiplex genome editing were about 60-70% and 20-40%, respectively. Compared with Nipponbare (Nip), CLCWR had higher Hygromycin-resistant callus frequency and transformation efficiency. Taken together, our study establishes a highly efficient transformation system for common wild rice with AA genome and provides a good rice material for de novo domestication by genome editing in the future.

Molecular and cytogenetic characterization of an Oryza officinalis-O. sativa chromosome 4 addition line and its progenies

The wild species Oryza officinalis Wall. ex Watt (2n = 24, CC) is a valuable genetic resource for rice (O. sativa L., 2n = 24, AA) breeding and genomics research. Genomic in situ hybridization (GISH) and molecular approaches were used to determine the nature and composition of the additional chromosome in a monosomic alien addition line (MAAL) of O. officinalis and its backcross progenies. The extra wild species chromosome in the MAAL (2n = 2x = 25) was a mosaic one, comprising of the long arm of chromosome 4 from O. officinalis and the short arm from O. sativa. Comparative analysis showed that O. sativa and O. officinalis shared high synteny of restriction fragment length polymorphism (RFLP) markers and low synteny of simple sequence repeat (SSR) markers. A DNA methylation alteration was revealed at C619 in the MAAL and progenies. Analysis of progenies of the MAAL indicated that introgression segments were small in size and introgression was not evenly distributed along the long arm. One recombination hot spot between C513 and RG177 was identified, which is in a gene-rich region.

Dynamics of gene introgression in the African malaria vector Anopheles gambiae

Anopheles gambiae is a major malaria vector in Africa and a popular model species for a variety of ecological, evolutionary, and genetic studies on vector control. Genetic manipulation of mosquito vectorial capacity is a promising new weapon for the control of malaria. However, the release of exotic transgenic mosquitoes will bring in novel alleles in addition to the parasite-inhibiting genes, which may have unknown effects on the local population. Therefore, it is necessary to develop methodologies that can be used to evaluate the spread rate of introduced genes in A. gambiae. In this study, the effects and dynamics of genetic introgression between two geographically distinct A. gambiae populations from western Kenya (Mbita) and eastern Tanzania (Ifakara) were investigated with amplified fragment length polymorphisms (AFLPs) and microsatellite markers. Microsatellites and polymorphic cDNA markers revealed a large genetic differentiation between the two populations (average F(ST) = 0.093, P < 0.001). When the two strains were crossed in random mating between the two populations, significant differences in the rate of genetic introgression were found in the mixed populations. Allele frequencies of 18 AFLP markers (64.3%) for Mbita and of 26 markers (92.9%) for Ifakara varied significantly from F5 to F20. This study provides basic information on how a mosquito release program would alter the genetic makeup of natural populations, which is critical for pilot field testing and ecological risk evaluation of transgenic mosquitoes.

Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by restriction fragment length polymorphism (RFLP) analysis and genomic in situ hybridization (GISH)

Restriction fragment length polymorphism (RFLP) analysis and GISH (genomic in situ hybridization) were performed on euploid plants derived from crosses between Oryza sativa (2n = 24, AA) and two brown planthopper-resistant accessions of O. eichingeri (2n = 24, CC). After screening with 164 RFLP markers, 60 of the 67 euploid plants were identified as introgression lines, each carrying 1–6 small O. eichingeri segments integrated on chromosomes 1, 2, 6, or 10. In the somatic chromosome preparations of F1 hybrid, O. eichingeri chromosomes, fluorescing greenish-yellow in the sequential GISH, appeared to be longer and to contain more heterochromatin than O. sativa ones, and this karyotypic polymorphism can be used to detect some introgressed O. eichingeri segments in euploid plants. In addition, GISH identification presented direct evidence for the transfer of small segments from O. eichingeri to O. sativa chromosome(s) which were subsequently recognized according to their condensation pattern, arm ratio, and chromosome length. The present results would contribute to the molecular mapping and selection of O. eichingeri - derived brown planthopper-resistant gene and positive yield QTLs.Key words: Oryza sativa, Oryza eichingeri, introgression lines, RFLP, genomic in situ hybridization (GISH).