title: Pseudo-backcrossing design for rapidly pyramiding multiple traits into a preferential rice variety.
abstract: BACKGROUND
  Pyramiding multiple genes into a desirable genetic background can take years to accomplish. In this paper, a pseudo-backcrossing scheme was designed to shorten the backcrossing cycle needed. PinK3, an aromatic and potentially high-yielding rice variety-although one that is intolerant to flash flooding (Sub) and susceptible to bacterial leaf blight (BB), leaf-neck blast (BL) and the brown planthopper (BPH)-was used as a genetic basis for significant improvements through gene pyramiding.
  
  
  RESULTS
  Four resistance donors with five target genes (Sub1A-C, xa5, Xa21, TPS and SSIIa) and three QTLs (qBph3, qBL1 and qBL11) were backcrossed individually using markers into the pseudo-recurrent parent 'PinK3' via one cycle of backcrossing followed by two cycles of pseudo-backcrossing and three selfings with rigorous foreground marker-assisted selection. In total, 29 pseudo-backcross inbred lines (BILs) were developed. Genome composition was surveyed using 61 simple sequence repeats (SSRs), 35 of which were located on six carrier chromosomes, with the remainder located on six non-carrier chromosomes. The recurrent genome content (%RGC) and donor genome content (%DGC), which were based on the physical positions of BC1F2, ranged from 69.99 to 88.98% and 11.02 to 30.01%, respectively. For the pseudo-BC3F3BILs, the %RGC and %DGC ranged from 74.50 to 81.30% and 18.70 to 25.50%, respectively. These results indicated that without direct background selection, no further increases in %RGC were obtained during pseudo-backcrossing, whereas rigorous foreground marker-assisted selection tended to reduce linkage drag during pseudo-backcrossing. The evaluation of new traits in selected pseudo-BC3F3BILs indicated significant improvements in resistance to BB, BL, BPH and Sub compared with PinK3, as well as significant improvements in grain yield (21-68%) over the donors, although yield was 7-26% lower than in 'PinK3'. All pyramided lines were aromatic and exhibited improved starch profiles, rendering them suitable for industrial food applications.
  
  
  CONCLUSIONS
  Results show that our new pyramiding platform, which is based on marker-assisted pseudo-backcrossing, can fix five target genes and three QTLs into a high-yielding pseudo-recurrent background within seven breeding cycles in four years. This multiple pseudo-backcrossing platform decreases the time required to generate new rice varieties exhibiting complex, durable resistance to biotic and abiotic stresses in backgrounds with desirable qualities.
authors.affiliation: Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140 Thailand ; Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Chatuchak, Bangkok 10900 Thailand.
authors.forename: Siriphat
authors.initials: S
authors.lastname: Ruengphayak
authors.affiliation: Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140 Thailand.
authors.forename: Ekawat
authors.initials: E
authors.lastname: Chaichumpoo
authors.affiliation: Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140 Thailand.
authors.forename: Supaporn
authors.initials: S
authors.lastname: Phromphan
authors.affiliation: Rice Gene Discovery, National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaengsaen, Nakhon Pathom 73140 Thailand.
authors.forename: Wintai
authors.initials: W
authors.lastname: Kamolsukyunyong
authors.affiliation: Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140 Thailand.
authors.forename: Wissarut
authors.initials: W
authors.lastname: Sukhaket
authors.affiliation: Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140 Thailand.
authors.forename: Ekapol
authors.initials: E
authors.lastname: Phuvanartnarubal
authors.affiliation: Rice Gene Discovery, National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaengsaen, Nakhon Pathom 73140 Thailand.
authors.forename: Siripar
authors.initials: S
authors.lastname: Korinsak
authors.affiliation: Rice Gene Discovery, National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaengsaen, Nakhon Pathom 73140 Thailand.
authors.forename: Siriporn
authors.initials: S
authors.lastname: Korinsak
authors.affiliation: Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140 Thailand ; Rice Gene Discovery, National Center for Genetic Engineering and Biotechnology (BIOTEC) National Science and Technology Development Agency (NSTDA), Kasetsart University, Kamphaengsaen, Nakhon Pathom 73140 Thailand ; Agronomy Department, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140 Thailand.
authors.forename: Apichart
authors.initials: A
authors.lastname: Vanavichit
keywords: Bacterial leaf blight resistance; Blast resistance; Brown planthopper resistance; Donor genome content; Gene pyramiding; Linkage drag; Multiple backcrossing; Pseudo-backcrossing; Recurrent genome content; Submergence tolerance
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