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Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct‑Seeded Rice

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Relation http://oar.icrisat.org/12560/
https://link.springer.com/article/10.1186/s12284-023-00665-w
https://doi.org/10.1186/s12284-023-00665-w
 
Title Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement
for Successful Crop Establishment in Deep Sown Direct‑Seeded Rice
 
Creator Sandhu, N
Ankush, A P
Singh, J
Raigar, O P
Bains, S
Jindal, T
Singh, M P
Sethi, M
Pruthi, G
Augustine, G
Verma, V K
Goyal, S
Kumar, Aman
Panwar, H
Sihag, M K
Kaur, R
Kurup, S
Kumar, A
 
Subject Rice
 
Description Background Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study.
Results Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations.
The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb
region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results
identified and validated seven potential candidate genes. The four promising introgression lines free from linkage
drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified.
Conclusion The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted
introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions
(2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs.
 
Publisher SpringerOpen
 
Date 2023-10-17
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12560/1/Rice_16_1-16_2023.pdf
Sandhu, N and Ankush, A P and Singh, J and Raigar, O P and Bains, S and Jindal, T and Singh, M P and Sethi, M and Pruthi, G and Augustine, G and Verma, V K and Goyal, S and Kumar, Aman and Panwar, H and Sihag, M K and Kaur, R and Kurup, S and Kumar, A (2023) Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct‑Seeded Rice. Rice, 16. pp. 1-16. ISSN 1939-8433