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Abstract We studied variation in adaptive traits and genetic association to understand the low P responses, including the symbiotic association of arbuscular mycorrhizal (AM) fungal colonization in Oryza species (O. sativa, O. nivara, and O. rufipogon). In the present experiment, we performed the phenotypic variability of the morphometric and geometric traits for P deficiency tolerance and conducted the association studies in GLM and MLM methods. A positive association between the geometric trait of the top-view area and root traits suggested the possibility of exploring a non-destructive approach in screening genotypes under low P. The AMOVA revealed a higher proportion of variation among the individuals as they belonged to different species of Oryza and the NM value was 2.0, indicating possible gene flow between populations. A sub-cluster with superior-performing accessions had a higher proportion of landraces (42.85%), and O. rufipogon (33.3%) was differentiated by four Pup1-specific markers. Association mapping identified seven notable markers (RM259, RM297, RM30, RM6966, RM242, RM184, and PAP1) and six potential genotypes (IC459373, Chakhao Aumbi, AC100219, AC100062, Sekri, and Kumbhi Phou), which will be helpful in the marker-assisted breeding to improve rice for P-deprived condition. In addition, total root surface area becomes a single major trait that helps in P uptake under deficit P up to 33% than mycorrhizal colonization. Further, the phenotypic analysis of the morphometric and geometric trait variations and their interactions provides excellent potential for selecting donors for improving P-use efficiency. The identified potential candidate genes and markers offered new insights into our understanding of the molecular and physiological mechanisms driving PUE and improving grain yield under low-P conditions.

Amino acid transporters (AATs) play a crucial role in facilitating the movement of amino acids across cellular membranes, which is vital for the growth and development of plants. Amino acid permease (AAP), which belongs to the AAT family, has been the subject of extensive functional research in plants. Although its importance is recognized, a comprehensive grasp of this family’s dynamics in indica rice remains lacking. In this investigation, a total of 27 AAP genes were identified in the genome of indica rice. Further, the phylogenetic analysis unveiled that the 69 AAP genes from both the model species and other plant species could be classified into 16 distinct subfamilies. The analysis of chromosomal mapping revealed an uneven distribution of the 27 OsAAP genes across the 12 rice chromosomes. Notably, the OsAAP family displayed a total of 10 duplicated gene pairs, along with the identification of numerous conserved motifs. The examination of cis-elements within OsAAP genes unveiled that their promoters contain cis-elements related to phytohormones, plant growth and development, as well as stress responses. Additionally, transcriptome profiling demonstrated that a substantial portion of these genes exhibited responsiveness to various hormones, with their activation spanning multiple tissues and developmental stages in rice. The study identified miRNAs with a specific affinity for OsAAP genes. Out of the 27 OsAAP genes investigated, seventeen were discovered to be targeted by a total of forty-three miRNAs. Furthermore, the aus allele of OsAAP3 that we named OsAAP17 was validated for its effect on productive tillers and yield, and seventeen genetic variants of OsAAP17 were found to be associated with a culm number in indica rice. In addition, indica rice varieties were monomorphic, while aus genotypes displayed polymorphism for OsAAP17 gene-specific in/dels. Moreover, in Season II (rabi season), it was found that the aus allele of OsAAP17 increased the number of productive tillers and the single plant yield by 22.55% and 9.67%, respectively, in a recombinant inbred population created by crossing N22 and JR 201. Remarkably, this enhancement was more pronounced during the dry cultivation season, highlighting the influence of environmental factors in the regulation of tiller numbers mediated by OsAAP17. The discoveries presented here lay a strong foundation for further exploration into the roles of OsAAP family genes across a range of developmental processes. Therefore, the identified allelic variations in the utilization of OsAAP17 has the potential to enhance rice crop production via molecular breeding in the changing climate scenario.

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.

Ranidhan is a popular late-maturing rice variety of Odisha state, India. The farmers of the state suffer heavy loss in years with flash floods as the variety is sensitive to submergence. Bacterial blight (BB) disease is a major yield-limiting factor, and the variety is susceptible to the disease. BB resistance genes Xa21, xa13, and xa5, along with the Sub1 QTL, for submergence stress tolerance were transferred into the variety using marker-assisted backcross breeding approach. Foreground selection using direct and closely linked markers detected the progenies carrying all four target genes in the BC1F1, BC2F1, and BC3F1 generations, and the positive progenies carrying these genes with maximum similarity to the recipient parent, Ranidhan, were backcrossed into each segregating generation. Foreground selection in the BC1F1 generation progenies detected all target genes in 11 progenies. The progeny carrying all target genes and similar to the recipient parent in terms of phenotype was backcrossed, and a total of 321 BC2F1 seeds were produced. Ten progenies carried all target genes/QTL in the BC2F1 generation. Screening of the BC3F1 progenies using markers detected 12 plants carrying the target genes. A total of 1270 BC3F2 seeds were obtained from the best BC3F1 progeny. Foreground selection in the BC3F2 progenies detected four plants carrying the target genes in the homozygous condition. The bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight pathogen. These BB pyramided lines were submergence-tolerant and similar to Ranidhan in 13 agro-morphologic and grain quality traits; hence, they are likely to be adopted by farmers.

Antioxidant-rich rice is a cheaper way to solve stress-related disorders and other health benefits for the global rice-eating population. Five antioxidant traits, namely, superoxide dismutase, flavonoids, anthocyanins, γ-oryzanol and 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) activity were mapped using a representative panel population through association mapping. Potential landraces carrying multiple antioxidant compounds were identified from the population. The population represented four genetic groups and correspondence for presence of antioxidants traits in each group was noticed. The population showed linkage disequilibrium for the studied traits based on the Fst values. A total of 14 significant marker–trait associations were detected for these antioxidant traits. The study validated the QTLs, qANC3 and qPAC12-2 for anthocyanin content and qAC12 for ABTS activity will be useful in marker-assisted breeding. Eleven QTLs such as qTAC1.1 and qTAC5.1 controlling anthocyanin content, qSOD1.1, qSOD5.1 and qSOD10.1 for superoxide dismutase (SOD), qTFC6.1, qTFC11.1 and qTFC12.1 for total flavonoids content (TFC), qOZ8.1 and qOZ11.1 for γ-oryzanol (OZ) and qAC11.1 for ABTS activity were detected as novel loci. Chromosomal locations on 11 at 45.3 cM regulating GO, TFC and TAC, and on the chromosome 12 at 101.8 cM controlling TAC and ABTS activity, respectively, were detected as antioxidant hotspots.

The rice variety ‘Swarna’ is highly popular in the eastern region of India. The farmers of eastern India cultivate mainly rainfed rice and face the adverse effects of climate change very frequently. Rice production in this region is not stable. Swarna variety is highly susceptible to bacterial blight (BB) disease and flash floods, which cause a heavy reduction in the yield. Transfer of five target genes/QTLs was targeted into the variety, Swarna by adopting marker-assisted backcross breeding approach. Direct markers for Sub1A, OsSPL14, and SCM2 QTLs and closely linked markers for xa5 and Xa21 BB resistance genes were screened in the backcross progenies. Swarna-Sub1, CR Dhan 800, and Swarna–Habataki near-isogenic lines (NILs) were used as donor parents in the breeding program. True multiple F1 plants were identified for backcrossing, and 796 BC1F1 seeds were generated. Foreground selection detected all the five target genes in six progenies in BC1F1 generation. The progeny containing all the target genes and more similar with the recipient parent was backcrossed, and a total of 446 BC2F1 seeds were produced. Foreground screening detected four BC2F1 plants carrying the five target genes. A total of 2,145 BC2F2 seeds were obtained from the best BC2F1 progeny. Screening of the progenies resulted in one plant with all five desirable genes, three plants with four, and another three progenies carrying three genes in homozygous conditions. The pyramided lines showed higher BB resistance and submergence tolerance than the recipient parent, Swarna. Culm strength of the pyramided lines showed higher breaking force than the recipient parent, Swarna. The pyramided line, SSBY-16-68-69 yielded the highest grain yield of 7.52 t/ha followed by the lines SSBY-16-68-511 (7.34 t/ha) and SSBY-16-68-1633 (7.02 t/ha). The best-pyramided line showed a yield advantage of 18% over the recipient parent and 6.8% over the yield component donor parent. Seven pyramided lines showed higher yield than the recipient parent, while five lines were better yielders than the yield component donor parent. The pyramided line SSBY-16-68-69 produced 365 grains/panicle, while the recipient had 152. The main morphologic and grain quality features of the recipient parent were retained in the pyramided lines.

Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. oryzae is a major biotic constraint on obtaining higher grain yields in rice. Marker-assisted backcross breeding (MABB) was performed by the pyramiding of Xa4, xa5, xa13 and Xa21 resistance genes in the popular variety, Ranidhan. A foreground selection in BC1F1, BC2F1, and BC3F1 progenies detected all the target genes in 12, 7 and 16 progenies by using the closely linked markers from a population size of 446, 410, and 530, respectively. The BB-positive progenies carrying the target genes with a maximal similarity to the recipient parent was backcrossed in each backcross generation. A total of 1784 BC3F2 seeds were obtained from the best BC3F1 progeny. The screening of the BC3F2 progenies for the four target genes resulted in eight plants carrying all the four target genes. A bioassay of the pyramided lines conferred very high levels of resistance to the predominant isolates of bacterial blight disease. In addition, these pyramided lines were similar to Ranidhan in 16 morpho-quality traits, namely, plant height, filled grains/panicle, panicles/plant, grain length, grain breadth, grain weight, milling, head rice recovery, kernel length after cooking, water uptake, the volume expansion ratio, gel consistency, alkali-spreading value, and the amylose content.

Submergence stress due to flash floods reduces rice yield drastically in sensitive varieties. Maudamani is a high yielding popular rice variety but is highly susceptible to submergence stress. The selection of progenies carrying Sub1 and GW5 (wide-grain) enhanced the submergence stress tolerance and grain yield of theMaudamani variety by following the marker-assisted backcross breeding method. Foreground screening detected 14 BC1F1, 17 BC2F1, and 12 BC3F1 backcross progenies that carried the target QTLs for submergence tolerance and grain width. Background screening was performed in the progenies carrying the target QTL and enhanced the recovery of a recipient parent’s genome by upto 96.875% in the BC3 pyramided line. The BC3F1 plant containing the highest recipient parent genome content and the target QTLs was self-pollinated. In BC3F2 generation, the target QTLs the Sub1 and GW5 (wide-grain) alleles and recipient parent’s yield component QTL OsSPL14 were tracked for homozygous states in the progenies. Seven pyramided lines showed tolerance to submergence for 14 days and higher grain yield than both the parents. The pyramided lines were similar to the recipient parent for the majority of the studied morphological and quality traits. The pyramided lines are useful as cultivars and can serve as potential donors for transfer of Sub1, OsSPL14, Gn1a, GW5 (wide-grain), and SCM2 QTLs.