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. 2023 Jun 27;24(13):10708.
doi: 10.3390/ijms241310708.

Transfer of Stress Resilient QTLs and Panicle Traits into the Rice Variety, Reeta through Classical and Marker-Assisted Breeding Approaches

Saumya Ranjan Barik  1 , Arpita Moharana  1 , Elssa Pandit  2 , Abhisarika Behera  1 , Ankita Mishra  1   3 , Shakti Prakash Mohanty  1 , Shibani Mohapatra  1   4 , Priyadarsini Sanghamitra  1 , Jitendriya Meher  1 , Dipti Ranjan Pani  5 , Vijai Pal Bhadana  6 , Shiv Datt  7 , Chita Ranjan Sahoo  3 , Reshmi Raj K R  1 , Sharat Kumar Pradhan  1   7
Affiliations

Transfer of Stress Resilient QTLs and Panicle Traits into the Rice Variety, Reeta through Classical and Marker-Assisted Breeding Approaches

Saumya Ranjan Barik et al. Int J Mol Sci. .

Abstract

Reeta is a popular late-maturing high-yielding rice variety recommended for cultivation in the eastern Indian states. The cultivar is highly sensitive to submergence stress. Phosphorus deficiency is an additional constraint for realizing high yield. The quantitative trait loci (QTLs), Sub1, for submergence and Pup1 for low phosphorus stress tolerance along with narrow-grained trait, GW5 were introgressed into the variety from the donor parent, Swarna-Sub1 through marker-assisted breeding. In addition, phenotypic selections for higher panicle weight, grain number, and spikelet fertility were performed in each segregating generation. Foreground selection detected the 3 target QTLs in 9, 8 and 7 progenies in the BC1F1, BC2F1, and BC3F1 generation, respectively. Recurrent parent's genome recovery was analyzed using 168 SSR polymorphic markers. The foreground analysis in 452 BC3F2 progenies showed five pyramided lines in homozygous condition for the target QTLs. No donor fragment drag was noticed in the Sub1 and GW5 QTLs carrier while a segmentwas observed in the Pup1 carrier chromosome. The developed lines were higher yielding, had submergence, and had low phosphorus stress-tolerance alongwith similar to the recipient parent in the studied morpho-quality traits. A promising pyramided line is released in the name of Reeta-Panidhan (CR Dhan 413) for the flood-prone areas of Odisha state.

Keywords: GW5; Pup1; Sub1; marker-assisted breeding; stress resilient; yield improvement.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
PCR amplification of markers Sub1A203 and Sub1BC2 linked to submergence tolerance; Pup1K46, RM28073 and RM28102 linked to low phosphorus tolerance genes along with grain yield marker GW5 in BC1F1 progenies. L: Molecular weight marker (50 bp plus ladder) and lanes on the top of the gel indicate BC1F1 progenies (RSS: Reeta Swarna-Sub1).
Figure 2
Figure 2
PCR amplification of markers Sub1A203 and Sub1BC2 linked to submergence tolerance; Pup1K46, RM28073 and RM28102 linked to low phosphorus tolerance genes along with grain yield marker GW5 in BC2F1 progenies. L: Molecular weight marker (50 bp plus ladder) and lanes on the top of the gel indicate BC1F1 progenies (RSS: Reeta Swarna-Sub1).
Figure 3
Figure 3
PCR amplification of markers Sub1A203 and Sub1BC2 linked to submergence tolerance; Pup1K46, RM28073 and RM28102 linked to low phosphorus tolerance genes along with grain yield marker GW5 in BC1F1 progenies. L: Molecular weight marker (50 bp plus ladder) and lanes on the top of the gel indicate BC3F1 progenies (RSS: Reeta Swarna-Sub1).
Figure 4
Figure 4
PCR amplification of markers Sub1A203 and Sub1BC2 linked to submergence tolerance; Pup1K46, RM28073 and RM28102 linked to low phosphorus tolerance genes along with grain yield marker GW5 in BC1F1 progenies. L: Molecular weight marker (50 bp plus ladder) and lanes on the top of the gel indicate BC3F2 progenies (RSS: Reeta Swarna-Sub1).
Figure 5
Figure 5
Seven pyramided lines of Swarna-Sub1 and Reeta along with parents in (A) dendrogram showing relatedness based on the 14 morphologic and quality traits; (B) Dendrogram showing the genetic relationship between lines based on 7 microsatellite markers and (C) % contribution of recurrent genome in the pyramided lines.
Figure 6
Figure 6
Analyses of QTLs stacking in carrier chromosomes associated with submergence tolerance, low phosphorus tolerance and yield component QTLs in the 5 pyramided lines (A) Sub1 QTL on the carrier chromosome 9 (B) Pup1 and (C) GW5 (narrow-grain) yield component QTLs on the carrier chromosome 5 present in the BC3F3 progenies of Reeta/Swarna-Sub1. The numbers indicate the pyramided lines, 1. RSS45-83-27-54, 2. RSS45-83-27-235, 3. RSS45-83-27-415, 4. RSS45-83-27-526, and 5. RSS45-83-27-648.
Figure 7
Figure 7
Percent of plants regenerated in the parental lines Reeta and Swarna-Sub1 and their pyramided lines carrying Sub1 QTL under control screening facility after one week of de-submergence from 14 days of submergence stress.
Figure 8
Figure 8
Successful introgression of Sub1 and Pup1 QTLs for stress resiliency and increased panicle yield in the flood-prone late-maturing rice using marker-assisted breeding. Photograph shows the panicles of parents, Reeta (right) and Swarna (left) along with the best pyramided lines (middle two) observed during the wet season, 2021.
Figure 9
Figure 9
The marker-assisted breeding scheme used for the development of pyramided lines for screening of submergence, low phosphorus stress tolerance, and panicle yield component QTLs. The numerical figures within parentheses indicate the number of hybrids/lines raised in the generation.
See this image and copyright information in PMC

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