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

Research

Smita Kurup¹  Harsh Panwar²  Manvesh Kumar Sihag²  Arvind Kumar³  Nitika Sandhu⁴  Gaurav Augustine⁴  Sutej Bains⁴  Gomsie Pruthi⁴  Vikas Kumar Verma⁴  Jasneet Singh⁴  Mohini Prabha Singh⁴  Om Prakash Raigar⁴  Aman Kumar⁴  Ade Pooja Ankush⁴  Shivani Goyal⁴  Rupinder Kaur⁴  Mehak Sethi⁴  Taveena Jindal⁴ 

[1] Department of Plant Science, Rothamsted Research, AL5 2JQ, Harpenden, Hertfordshire, UK;Guru Angad Dev Veterinary and Animal Sciences University, 141004, Ludhiana, Punjab, India;International Rice Research Institute (IRRI) South Asia Regional Centre (ISARC), 221106, Varanasi, Uttar Pradesh, India;International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), 502324, Patancheru, Telangana, India;Punjab Agricultural University, 141004, Ludhiana, Punjab, India;

关键词: Direct seeded rice;    Gene;    Mesocotyl elongation;    QTL mapping;    Seedling vigor;    Transcriptome;   

DOI  :  10.1186/s12284-023-00665-w

 received in 2023-08-30, accepted in 2023-10-12,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundOngoing 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.ResultsSignificant 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.ConclusionThe 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.

【 授权许可】

CC BY   
© Springer Science+Business Media, LLC, part of Springer Nature 2023

【 图 表 】

12951_2015_155_Article_IEq9.gif

Fig. 10

Fig. 1

Fig. 1

Fig. 4