Root attributes governing drought stress adaptation and the associated molecular markers in chromosome segment substitution lines in rice (Oryza sativa L.)

The wild relatives of cultivated rice offer crucial resistance genes for combating stresses like drought. Developing rice varieties with drought tolerance is possible through chromosome segment substitution lines (CSSLs), which blend the genetic background of a high-yielding parent with specific chromosome segments from a donor parent. This study aimed to study the effect of drought stress on various root traits of chromosome segment substitution lines (CSSLs) and their relationship with specific molecular markers. Ninety-six genotypes, including 80 chromosome segment substitution lines (Curinga x O. rufipogon and Curinga x O. meridionalis), 9 New Rice for Africa (NERICAs) and 7 controls were grown in Basket and PVC pipe methods for phenotyping different root traits. Under drought stress (DS), MER16, MER20, RUF10, RUF16, RUF44, NERICA1, and NERICA3 showed superior performance for most of the root traits. These evaluations were supplemented with association analysis of 17 root trait-linked simple sequence repeat (SSR) markers with root phenotypic traits. The marker RM201 is strongly associated with multiple root traits, found to be independent of three growth conditions (well-watered “WW” under Basket, WW condition and DS conditions under PVC pipe). The marker RM316 is associated with root volume, and the marker RM7424 and RM1054 show maximum root length. In conclusion, these markers can be used in marker-assisted breeding programs, and the lines carrying them can be used as parental lines in variety-development programs for drought tolerance

Development of Broad Spectrum and Durable Bacterial Blight Resistant Variety through Pyramiding of Four Resistance Genes in Rice

Not AvailableBacterial 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 426, 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.Not Availabl

Marker-Assisted Backcross Breeding for Improvement of Submergence Tolerance and Grain Yield in the Popular Rice Variety, ‘Maudamani’

Abstract Background: Submergence stress due to flash flood reduces rice yield drastically in sensitive varieties. Maudamani is a high yielding popular rice variety but highly susceptible to submergence stress. The Sub1 and yield component QTL, GW5 were transferred into the popular high yielding variety for enhancing submergence tolerance and yield. Methods: Sub1 and GW5 QTLs were transferred into Maudamani variety by adopting marker-assisted backcross breeding method. The target QTLs were selected by foreground selection in each backcross generation progenies to track the target QTLs. Recipient parent’s genome recovery was accelerated by adopting background selection in each backcross generation progenies carrying the target QTLs. Results: The two target QTLs were tracked in each backcross generation progenies by employing the tightly linked and direct markers. Background screening was performed in each backcross generation progenies carrying the target QTLs by using 57 background markers for enhancing the recovery of recipient parent’s genome content. The selected progenies containing highest genome recovery of the parent was hybridized with recipient parent, Maudamani. Finally, the selected BC3F1 plant containing highest recipient parent genome content and the two target QTLs was self-pollinated. In BC3F2 generation, two QTLs, Sub1 and GW5 along with recipient parent’s yield component QTLs, OsSPL14, Gn1a and SCM2 were tracked for their homozygous state in the progenies. Amongst the developed pyramided lines, six lines showed tolerance to submergence for 14 days and also exhibited higher grain yield than both the parents. The pyramided lines, MSS 607-116-541-117 and MSS 607-116-541-436 produced &gt;9 t/ha grain yield showing an advantage of &gt;5% over the popular recipient variety. Few pyramided lines were similar in appearance and quality traits with the recipient parent. Conclusion: The pyramided lines will be useful as potential donors for the QTLs Sub1+ OsSPL14+ Gn1a + GW5 + SCM2 and also as cultivars.</jats:p

Application of Statistical Tools for Data Analysis and Interpretation in Rice Plant Pathology

There has been a significant advancement in the application of statistical tools in plant pathology during the past four decades. These tools include multivariate analysis of disease dynamics involving principal component analysis, cluster analysis, factor analysis, pattern analysis, discriminant analysis, multivariate analysis of variance, correspondence analysis, canonical correlation analysis, redundancy analysis, genetic diversity analysis, and stability analysis, which involve in joint regression, additive main effects and multiplicative interactions, and genotype-by-environment interaction biplot analysis. The advanced statistical tools, such as non-parametric analysis of disease association, meta-analysis, Bayesian analysis, and decision theory, take an important place in analysis of disease dynamics. Disease forecasting methods by simulation models for plant diseases have a great potentiality in practical disease control strategies. Common mathematical tools such as monomolecular, exponential, logistic, Gompertz and linked differential equations take an important place in growth curve analysis of disease epidemics. The highly informative means of displaying a range of numerical data through construction of box and whisker plots has been suggested. The probable applications of recent advanced tools of linear and non-linear mixed models like the linear mixed model, generalized linear model, and generalized linear mixed models have been presented. The most recent technologies such as micro-array analysis, though cost effective, provide estimates of gene expressions for thousands of genes simultaneously and need attention by the molecular biologists. Some of these advanced tools can be well applied in different branches of rice research, including crop improvement, crop production, crop protection, social sciences as well as agricultural engineering. The rice research scientists should take advantage of these new opportunities adequately in adoption of the new highly potential advanced technologies while planning experimental designs, data collection, analysis and interpretation of their research data sets

Genetic Mapping Of Morpho-Physiological Traits Involved During Reproductive Stage Drought Tolerance In Rice

AbstractReproductive stage drought stress is an important factor for yield reduction in rice. Genetic mapping of drought responsive QTLs will help to develop cultivars suitable for drought prone environments through marker-assisted breeding. QTLs linked to morpho-physiological traits under drought stress were mapped by evaluating 190 F7 recombinant inbred lines (RIL). Significant variations were observed for eleven morpho-physiological traits involved during the stress. Bulked segregant analysis (BSA) strategy was adopted for genotyping the RIL population. A total of 401 SSR primers were tested for parental polymorphism of which 77 were polymorphic. Inclusive composite interval mapping detected a total of five consistent QTLs controlling leaf rolling (qLR9.1), leaf drying (qLD9.1), harvest index (qHI9.1), spikelet fertility (qSF9.1) and relative water content (qRWC9.1) under reproductive stage drought stress. Another two non-allelic QTLs controlling leaf rolling (qLR8.1) and leaf drying (qLD12.1) were linked in a single year. QTL controlling leaf rolling, qLR8.1 was validated in this mapping population and useful in marker-assisted breeding (MAB) programs. Out of these five consistent QTLs, four (qLR9.1, qLD9.1, qHI9.1 and qRWC9.1) were detected to be novel QTLs and useful for MAB for reproductive stage drought tolerance in rice.</jats:p

Genetic mapping of morpho-physiological traits involved during reproductive stage drought tolerance in rice.

Reproductive stage drought stress is an important yield reducing factor in rainfed rice. Genetic mapping of morpho-physiological traits under the stress will help to develop cultivars suitable for drought prone environments through marker-assisted breeding (MAB). Though various yield QTLs under reproductive stage drought tolerance are available for MAB, but no robust markers controlling different morho-physiological traits are available for this stress tolerance. QTLs linked to morpho-physiological traits under drought stress were mapped by evaluating 190 F7 recombinant inbred lines (RIL) using bulk segregant analysis (BSA) strategy. Wide variations were observed in the RILs for eleven morpho-physiological traits involved during the stress. A total of 401 SSR primers were surveyed for parental polymorphism of which 77 were detected to be polymorphic. Inclusive composite interval mapping detected a total of five consistent QTLs controlling leaf rolling (qLR9.1), leaf drying (qLD9.1), harvest index (qHI9.1), spikelet fertility (qSF9.1) and relative water content (qRWC9.1) under reproductive stage drought stress. Another two non-allelic QTLs controlling leaf rolling (qLR8.1) and leaf drying (qLD12.1) were also detected to be linked and found to control the two traits. QTL controlling leaf rolling, qLR8.1 was validated in this mapping population and may be useful in MAB programs. Out of these five consistent QTLs, four (qLR9.1, qLD9.1, qHI9.1 and qRWC9.1) were detected to be novel QTLs and useful for MAB for improvement of reproductive stage drought tolerance in rice