QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems

Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3–17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7–15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4’s effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited

Development of Oryza sativa L. by Oryza punctata Kotschy ex Steud. monosomic addition lines with high value traits by interspecific hybridization

Oryza punctata\ua0is a distantly related wild\ua0Oryza\ua0species having BB genome with untapped genetic resources for rice improvement. Low crossability between the cultivated\ua0O. sativa\ua0and\ua0O. punctata\ua0restricts the success of transferring many desirable traits into cultivated rice. Artificially induced autotetraploids of an elite breeding line, IR31917-45-3-2, were produced and crossed with\ua0O. punctata. Allotriploid F1\ua0plants were backcrossed to IR31917-45-3-2 and generated progenies with extra chromosomes from\ua0O. punctata. Twenty BC1F1\ua0and 59 BC2F1\ua0plants were produced with chromosome numbers ranging from 24 (2n) to 29 (2n\ua0+\ua05) and 2n\ua0(24) to 26 (2n\ua0+\ua02), respectively. Eleven monosomic alien addition lines (MAALs) were characterized morphologically and cytologically and designated as MAAL 1–12. MAALs were genotyped using\ua0O. punctata\ua0genome-specific molecular markers and detected chromosome segments inherited from\ua0O. punctata.\ua0O. punctata\ua0introgressions across all the chromosomes of\ua0O. sativa\ua0were identified except for chromosome 8. The most frequent introgressions were observed in chromosomes 4, 6, 10, and 11, which could be the recombination hotspots between A and B genomes. Some of the qualitative traits such as black hull, purple coleoptile base, purple stigma, long awn, and short grain size from\ua0O. punctata\ua0were inherited in some disomic introgression lines (DILs). Several DILs inherited genes from\ua0O. punctata\ua0conferring resistance to brown planthopper, green leafhopper, and diseases such as bacterial blight and blast. This is the first report on successful gene transfer from\ua0O. punctata\ua0into\ua0O. sativa

Exploring Key Blast and Bacterial Blight Resistance Genes in Genetically Diverse Rice Accessions through Molecular and Phenotypic Evaluation

Blast and bacterial blight (BB) are the most dangerous rice (Oryza sativa\ua0L.) diseases that limit rice production significantly.\ua0Pib,\ua0Piz‐t, and\ua0Pi9\ua0are reported as key resistance genes for blast whereas\ua0Xa21,\ua0Xa4,\ua0Xa7, and\ua0xa13\ua0are considered as important resistance genes for BB. Using gene‐specific DNA markers, the presence of these resistance genes was screened in 211 diverse rice accessions originating from 26 countries. In molecular marker analyses, specific amplification patterns for the\ua0Pib\ua0and\ua0Piz‐t\ua0resistance alleles were observed in 56 and 23 accessions, respectively, whereas the\ua0Pi9\ua0resistance allele was not observed at all in these accessions. For BB, at least one BB resistance gene was present in 148 of the 211 evaluated accessions. All 211 accessions were evaluated for blast resistance using natural isolates and for BB resistance using Race 4 (PX071) and Race 6 (PX099). Among 211 accessions, 89 exhibited hypersensitive blast resistance reactions, whereas 85 and 37 accessions were rated as resistant or moderately resistance to BB Races 4 and 6, respectively. The combined analysis of molecular and phenotypic reactions (marker‐trait association assay) revealed that landraces possessed rare and several desirable genes compared with breeding lines with a narrow genetic base, hence these landraces serve as the valuable source for exploring new resistance genes for crop improvement. An interesting similarity in gene distribution pattern was observed in\ua0Pib\ua0with\ua0Xa21\ua0and in\ua0Piz‐t\ua0with\ua0Xa7. The analyzed blast and BB resistance genes were in a range of combinations in different landraces and breeding lines, which can be used in gene introgression and pyramiding programs as alternative resistance sources

Development of an intergeneric hybrid between Oryza sativa L. and Leersia perrieri (A. Camus) Launert

An intergeneric hybrid was successfully developed between\ua0Oryza sativa\ua0L. (IRRI 154) and\ua0Leersia perrieri\ua0(A. Camus) Launert using embryo rescue technique in this study. A low crossability value (0.07%) implied that there was high incompatibility between the two species of the hybrid. The F1\ua0hybrid showed intermediate phenotypic characteristics between the parents but the plant height was very short. The erect plant type resembled the female parent IRRI 154 but the leaves were similar to\ua0L. perrieri. Cytological analysis revealed highly non-homology between chromosomes of the two species as the F1\ua0plants showed 24 univalents without any chromosome pairing. The F1\ua0hybrid plant was further confirmed by PCR analysis using the newly designed 11 indel markers showing polymorphism between\ua0O. sativa\ua0and\ua0L. perrieri. This intergeneric hybrid will open up opportunities to transfer novel valuable traits from\ua0L. perrieri\ua0into cultivated rice

Newly Identified Wild Rice Accessions Conferring High Salt Tolerance Might Use a Tissue Tolerance Mechanism in Leaf

Cultivated rice (Oryza sativa\ua0L.) is very sensitive to salt stress. So far a few rice landraces have been identified as a source of salt tolerance and utilized in rice improvement. These tolerant lines primarily use Na+\ua0exclusion mechanism in root which removes Na+\ua0from the xylem stream by membrane Na+\ua0and K+\ua0transporters, and resulted in low Na+\ua0accumulation in shoot. Identification of a new donor source conferring high salt tolerance is imperative. Wild relatives of rice having wide genetic diversity are regarded as a potential source for crop improvement. However, they have been less exploited against salt stress. Here, we simultaneously evaluated all 22 wild\ua0Oryza\ua0species along with the cultivated tolerant lines including Pokkali, Nona Bokra, and FL478, and sensitive check varieties under high salinity (240 mM NaCl). Based on the visual salt injury score, three species (O.\ua0alta, O.\ua0latifolia, and\ua0O.\ua0coarctata) and four species (O.\ua0rhizomatis, O.\ua0eichingeri, O.\ua0minuta, and\ua0O.\ua0grandiglumis) showed higher and similar level of tolerance compared to the tolerant checks, respectively. All three CCDD genome species exhibited salt tolerance, suggesting that the CCDD genome might possess the common genetic factors for salt tolerance. Physiological and biochemical experiments were conducted using the newly isolated tolerant species together with checks under 180 mM NaCl. Interestingly, all wild species showed high Na+\ua0concentration in shoot and low concentration in root unlike the tolerant checks. In addition, the wild-tolerant accessions showed a tendency of a high tissue tolerance in leaf, low malondialdehyde level in shoot, and high retention of chlorophyll in the young leaves. These results suggest that the wild species employ tissue tolerance mechanism to manage salt stress. Gene expression analyses of the key salt tolerance-related genes suggested that high Na+\ua0in leaf of wild species might be affected by\ua0OsHKT1;4-mediated Na+\ua0exclusion in leaf and the following Na+\ua0sequestration in leaf might be occurring independent of tonoplast-localized OsNHX1. The newly isolated wild rice accessions will be valuable materials for both rice improvement to salinity stress and the study of salt tolerance mechanism in plants

Back to the wild: on a quest for donors toward salinity tolerant rice

Salinity stress affects global food producing areas by limiting both crop growth and yield. Attempts to develop salinity-tolerant rice varieties have had limited success due to the complexity of the salinity tolerance trait, high variation in the stress response and a lack of available donors for candidate genes for cultivated rice. As a result, finding suitable donors of genes and traits for salinity tolerance has become a major bottleneck in breeding for salinity tolerant crops. Twenty-two wild Oryza relatives have been recognized as important genetic resources for quantitatively inherited traits such as resistance and/or tolerance to abiotic and biotic stresses. In this review, we discuss the challenges and opportunities of such an approach by critically analyzing evolutionary, ecological, genetic, and physiological aspects of Oryza species. We argue that the strategy of rice breeding for better Na exclusion employed for the last few decades has reached a plateau and cannot deliver any further improvement in salinity tolerance in this species. This calls for a paradigm shift in rice breeding and more efforts toward targeting mechanisms of the tissue tolerance and a better utilization of the potential of wild rice where such traits are already present. We summarize the differences in salinity stress adaptation amongst cultivated and wild Oryza relatives and identify several key traits that should be targeted in future breeding programs. This includes: (1) efficient sequestration of Na in mesophyll cell vacuoles, with a strong emphasis on control of tonoplast leak channels; (2) more efficient control of xylem ion loading; (3) efficient cytosolic K retention in both root and leaf mesophyll cells; and (4) incorporating Na sequestration in trichrome. We conclude that while amongst all wild relatives, O. rufipogon is arguably a best source of germplasm at the moment, genes and traits from the wild relatives, O. coarctata, O. latifolia, and O. alta, should be targeted in future genetic programs to develop salt tolerant cultivated rice