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Identification of Yield Enhancement Qtls (2009-10)

Dr.Mrs Hosneara Hossain
SSO
Biotechnology Division, BRRI, Gazipur

Md.Monirul Islam
SSO
Biotechnology Division, BRRI, Gazipur

Ripon Kumar Roy
SO
Biotechnology Division, BRRI, Gazipur

Dr,Md.Enamul Hoque
CSO and Head (In Charge )
Biotechnology Division, BRRI, Gazipur

Dr. Md. Shamsher Ali
CSO
Biotechnology Division, BRRI, Gazipur

Abstract/ Executive Summary:

Wild species of crop plants are increasingly being used to improve various agronomic traits including yield in cultivars. Advanced backcross QTL analysis has been used to identify naturally occurring favorable QTL alleles for yield. BRRI dhan28 and BRRI dhan29 were used as recurrent parents. Two advanced backcross populations BC2F2 will be developed through cross between BR28*3/ Oryza rufipogon and BR29*3/O.rufipogon. Two accessions of O. rufipogon( 103403 and 10589) has been used. A total of 942 BC1F1 seeds were obtained after backcrossing .A total of 100 simple sequence repeat (SSR) markers were screened for polymorphism between the parents. Among them 35 primers showed polymorphism. Markers those detected polymorphism between the two parents were used for molecular analysis of the population. The rate of polymorphism was more than 50% indicated high genetic diversity between parents which originated from cultivated and wild species.

Keywords: Population, QTL analysis, Backcrosses

Location: Biotechnology Division, BRRI-Gazipur

Start Date: 01-07-2008

End Date: 01-01-2011

Program Area: Variety and Species

Commodity: Rice

Objectives:

1. To identify yield enhancement QTL from a wild relative of rice Oryza rufipogon.
2. To enhance the grain yield of elite Bangladeshi rice variety through the introgression of yield-enhancing QTLs.
3. To broaden genetic basis of cultivated rice.

Methodology:

BRRI dhan28 and BRRI dhan29 were used as recurrent parents. Two advanced backcross populations BC2F2 will be developed through cross between BR28*3/ Oryza rufipogon and BR29*3/O.rufipogon. Two accessions of O. rufipogon( 103403 and 10589) has been used. Population development: A single plant of O. rufipogon served as a male parent in crosses using BRRI dhan28 and BRRI dhan29 individuals. F1 plants were grown in net house and three most vigorous F1 plants were backcrossed to BRRI dhan28 and BRRI dhan29 (as male), from which BC1F1 seeds were collected. Second round of backcrossing will be carried out with BRRI dhan28 and seeds of BC2F1 will be collected from which some BC2F1 seeds will be grown in the fields and subsequently best plants will be selected and harvested individually based on phenotype to generate BC2F2 seeds. Trait evaluation: Phenotypic measurements will be performed for 12 traits, as follows: (1) days to heading; (2) plant height; (3) grains per panicle; (4) percent seed set; (5) panicle length; (6) panicles per plant (7) grain weight; (8) yield per plant; (9) spikelets per panicle; (10) shattering; (11) awns from no awns to awns over 1 cm in length; (12) tiller type. Genotyping: For polymorphic survey, parents, BRRI dhan28 , BRRI dhan29 and Two accessions of O. rufipogon: 103403 and 10589 were used. DNA was extracted from young leaves of 21 days old plants by mini DNA prep. method. The concentration of extracted DNA was estimated by Nano Drop Spectrophotometer. Each PCR was carried out in a 10 μL reaction volume containing 1 μL of MgCl2 free 10X PCR buffer, 1.2 μL of 25 mM MgCl2, 0.2 μL of 10 mM dNTPs, 0.2 μL of 5 U/μL Taq DNA polymerase, 0.5 μL of 10 μM forward and reverse primers and 2 μL (10ng) of DNA using a 96 well thermal cycler (G-Storm). The temperature profile use for PCR amplification comprised of 94° C for 5 min (initial denaturation) followed by 35 cycles of 94° C for 1 min (denaturation), 55° C for 1 min (annealing), 72° C for 2 min (extension) and a final extension for 7 min at 72° C at the end of 35 cycles. The annealing temperatures were adjusted based on the specific requirements of each primer combination. The PCR products were mixed with gel loading dye and electrophoresed in 8% polyacrylamide gel using vertical polyacrylamide gels for high throughput manual genotyping. Four micro liters of amplification products were resolved by running gel in 1X TBE buffer for 1.5 - 2.5 hrs depending upon the allele size at around 75 volts and 180 mA electricity. The gels were stained in 1 μg/ml ethidium bromide solution and were documented using UVPRO (Uvipro Platinum, EU) gel documentation unit. Parental polymorphism and QTL analysis: A set of 500 microsatellite markers spanning all the 12 rice chromosomes will be screened between O. rufipogon and BRRI dhan28; O. rufipogon and BRRI dhan29. Microsatellite or Simple sequence repeat (SSR) primers are used for selection (Temnykh et al. 2001; McCouch et al. 2002; IRGSP 2005). A total of 100 polymorphic microsatellite markers will be separated which will be evenly spaced through out the genome. To identify the QTLs for yield and yield components, QTL analyses will be performed by using Window based WinQTL Cartographer version 2.5 software (Wang et al., 2005)/ QGene version 4.3. Each marker will be analyzed to determine the regions associated with the trait.

Source of Information: Proceedings of the BRRI Annual Internal Review for (2009-10)

Article Link (Online Journal):

Funding Source:

1. Government

Budget:

Total Budget (Tk.) :

Achievement/Findings:

A total of 942 BC1F1 seeds were obtained after backcrossing .A total of 100 simple sequence repeat (SSR) markers were screened for polymorphism between the parents. Among them 35 primers showed polymorphism. Markers those detected polymorphism between the two parents were used for molecular analysis of the population. The rate of polymorphism was more than 50% indicated high genetic diversity between parents which originated from cultivated and wild species.

Knowledge Management: Report/Proceedings