Mapping of Qtl for Anaerobic Germination Using the Donor Ac39416a in the Genetic Background of Swarna Sub-1 (Oryza Sativa L.)

Background: Anaerobic germination is an important trait in particular for cultivation under direct seeding method in kharif season, as well as during nursery rising for transplant rice, as sometimes unexpected rains immediately after sowing will drastically reduce the plant population.Methods and Results: In the present investigation phenotypic screening for Anaerobic germination (AG) was carried out using 188 F2:3 population of Swarna Sub1/AC39416A at RARS (APRRI), Maruteru. The mean anaerobic germination per cent recorded after the two weeks of submergence ranged from 0% to 95% with overall mean of 47.51% whereas, for three weeks of submergence, the mean anaerobic germination per cent recorded between 0 and 95%, with overall mean of 37.66%. 134 (19.42%) out of 687 Simple Sequence Repeats (SSR) markers surveyed were polymorphic between the parents. Linkage analysis was done with 83 SSR markers showing polymorphism clearly using the integrated software called QTL IciMapping software version 4.1.0. The length of linkage map constructed across whole genome was 3600.8 cM and identified seven QTLs viz., qAG2, qAG3, qAG7-1, qAG7-2, qAG9, qAG10 and qAG12. All these seven QTLs explained phenotypic variance of about 37.47% collectively for AG trait, with their individual contributions ranging from 3.5% to 8.67% of phenotypic variation and LOD scores of 2.6 to 5.86. The LOD score and phenotypic variance is 5.86 and 8.67% respectively for qAG10 a novel QTL identified in the present study using ICIM method. Conclusion: QTL “qAG12-1” identified in this study may be considered for introgression into popular elite rice varieties otherwise susceptible for anaerobic germination after fine mapping studies.

Penampilan Agronomi Galur-Galur Padi Sawah Tadah Hujan Toleran Kondisi Anaerob pada Fase Perkecambahan

Budidaya padi di sawah tadah hujan dengan sistem tebar benih langsung memerlukan varietas yang beradaptasi baik pada kondisi ekosistem tersebut dan toleran terhadap tingkat oksigen rendah selama berkecambah atau anaerobic germination (AG). Penelitian bertujuan mengevaluasi penampilan agronomi galur-galur padi dilakukan di sawah tadah hujan, serta toleransinya terhadap kondisi AG. Evaluasi toleransi cekaman kondisi anaerob dilakukan di rumah kaca BB Padi pada bulan Februari 2020. Materi yang digunakan adalah 12 genotipe padi. Penapisan AG dilakukan dengan merendam benih dalam air dengan ketinggian 10 cm selama 10 hari. Pengujian daya hasil dilakukan di sawah tadah hujan Sumedang dan Pati pada musim hujan 2020. Percobaan disusun menggunakan rancangan kelompok lengkap teracak dengan empat ulangan. Toleransi terhadap kondisi AG dapat diidentifikasi berdasarkan karakter persentase daya pulih, panjang tunas dan akar, dan biomassa. Karakter-karakter tersebut saling berkorelasi nyata, positif, dan kuat. Galur IR 83381-B-B-6-1, IR 129336:11-19-Ski-0-Kn-3 dan B14897E-SKI-9-7-2 memiliki toleransi AG lebih baik daripada Inpari 30 dan Inpari 39. Dari hasil pengujian lapangan, dua galur memiliki rata-rata GKG setara dengan Inpari 30 dan Inpari 39, serta konsisten cukup tinggi yaitu IR 129336:11-19-Ski-0-Kn-3 (5.61 ton ha-1) dan B14316E-KA-15 (6.04 ton ha-1). Hasil pengujian ini dapat dilanjutkan dengan uji multi lokasi pada galur IR 83381-B-B-6-1, IR 129336:11-19-Ski-0-Kn-3 dan B14897E-SKI-9-7-2 dengan mempertimbangkan daya hasil dan adaptasinya sehingga dapat dilepas menjadi varietas toleran AG. Kata kunci: cekaman abiotik, perkecambahan anaerob, tebar benih langsung

Enriched-GWAS and Transcriptome Analysis to Refine and Characterize a Major QTL for Anaerobic Germination Tolerance in Rice

Tolerance of anaerobic germination (AG) is a key trait in the development of direct seeded rice. Through rapid and sustained coleoptile elongation, AG tolerance enables robust seedling establishment under flooded conditions. Previous attempts to fine map and characterize AG2 (qAG7.1), a major centromere-spanning AG tolerance QTL, derived from the indica variety Ma-Zhan Red, have failed. Here, a novel approach of “enriched haplotype” genome-wide association study based on the Ma-Zhan Red haplotype in the AG2 region was successfully used to narrow down AG2 from more than 7 Mb to less than 0.7 Mb. The AG2 peak region contained 27 genes, including the Rc gene, responsible for red pericarp development in pigmented rice. Through comparative variant and transcriptome analysis between AG tolerant donors and susceptible accessions several candidate genes potentially controlling AG2 were identified, among them several regulatory genes. Genome-wide comparative transcriptome analysis suggested differential regulation of sugar metabolism, particularly trehalose metabolism, as well as differential regulation of cell wall modification and chloroplast development to be implicated in AG tolerance mechanisms.

Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice

Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs.

Dynamic genome-wide association analysis and identification of candidate genes involved in anaerobic germination tolerance in rice

Background In Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding. Results In this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (−log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19–1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG. Conclusion The four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.