Abstract
BackgroundMarker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity. MAS will need to address concerns about the population size needed to introgress together more than two genes/QTLs. In the present study, grain yield and genotypic data from different generations (F3 to F8) for five marker-assisted breeding programs were analyzed to understand the effectiveness of synergistic effect of phenotyping and genotyping in early generations on selection of better progenies.ResultsBased on class analysis of the QTL combinations, the identified superior QTL classes in F3/BC1F3/BC2F3 generations with positive QTL x QTL and QTL x background interactions that were captured through phenotyping maintained its superiority in yield under non-stress (NS) and reproductive-stage drought stress (RS) across advanced generations in all five studies. The marker-assisted selection breeding strategy combining both genotyping and phenotyping in early generation significantly reduced the number of genotypes to be carried forward. The strategy presented in this study providing genotyping and phenotyping cost savings of 25–68% compared with the traditional marker-assisted selection approach. The QTL classes, Sub1 + qDTY1.1 + qDTY2.1 + qDTY3.1 and Sub1 + qDTY2.1 + qDTY3.1 in Swarna-Sub1, Sub1 + qDTY1.1 + qDTY1.2, Sub1 + qDTY1.1 + qDTY2.2 and Sub1 + qDTY2.2 + qDTY12.1 in IR64-Sub1, qDTY2.2 + qDTY4.1 in Samba Mahsuri, Sub1 + qDTY3.1 + qDTY6.1 + qDTY6.2 and Sub1 + qDTY6.1 + qDTY6.2 in TDK1-Sub1 and qDTY12.1 + qDTY3.1 and qDTY2.2 + qDTY3.1 in MR219 had shown better and consistent performance under NS and RS across generations over other QTL classes.Conclusion“Deployment of this procedure will save time and resources and will allow breeders to focus and advance only germplasm with high probability of improved performance. The identification of superior QTL classes and capture of positive QTL x QTL and QTL x background interactions in early generation and their consistent performance in subsequent generations across five backgrounds supports the efficacy of a combined MAS breeding strategy”.
Highlights
Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity
The grain yield advantage ranged from 48.0 to 2216.9 kg ha− 1 and 95.5 to 1296.4 kg ha− 1 under NS and reproductive-stage drought stress (RS) drought stress conditions, respectively, in Samba Mahsuri introgressed with qDTY2.2 + qDTY4.1 (Table 3)
A grain yield reduction of 68, 93, 98, and 96% was observed in F4, F6, F7, and F8 generations, respectively, under RS drought stress compared with NS in TDK1-Sub1 introgressed lines
Summary
Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity. MAS will need to address concerns about the population size needed to introgress together more than two genes/QTLs. In the present study, grain yield and genotypic data from different generations (F3 to F8) for five marker-assisted breeding programs were analyzed to understand the effectiveness of synergistic effect of phenotyping and genotyping in early generations on selection of better progenies. We were able to understand the effectiveness of early generation selection in the marker-assisted introgression program for drought because the breeding program maintained systematic data for both genotyping and phenotyping conducted over the past six or more years It was only after we successfully identified the best lines coming from each introgression program after successful multi-location evaluation that we realized that, as the breeding program will need to bring in more and more genes for multiple traits to address each of the new emerging climate-related challenges, modifications that allow plant breeders to make large-scale rejections in the early generation will become necessary. The effectiveness of the combined MAS strategy is evident from the result that, in none of the five cases were the superior QTL class combinations identified in F3 outperformed by inferior classes identified in F3 in any advanced generation under both NS and variable intensities of RS drought stress in different seasons/years across generations from F4 to F6/F7/F8
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