QTL Mapping And Candidate Gene Mining of Flag Leaf Size Traits In Japonica Rice Based On Linkage Mapping And Genome-Wide Association Study

As one of the most important part of the ideal plant type of japonica rice, leaf shape affects the photosynthesis and carbohydrate accumulation directly. Mining and using new leaf shape related genes/QTLs can further enrich the theory of molecular breeding and accelerate the breeding process of japonica rice. In the present study, 2 RILs and a natural population with 295 japonica rice varieties were used to map QTLs for flag leaf length (FL), flag leaf width (FW) and flag leaf area (FLA) by linkage analysis and genome-wide association study (GWAS) through 2 years. A total of 64 QTLs were detected by 2 ways, and pleiotropic QTLs qFL2 (Chr2_33,332,579) and qFL10 (Chr10_10,107,835; Chr10_10,230,100) consisted of overlapping QTLs mapped by linkage analysis and GWAS through 2 years were identified. The candidate genes LOC_Os02g54254, LOC_Os02g54550, LOC_Os10g20160, LOC_Os10g20240, LOC_Os10g20260 were obtained, filtered by linkage disequilibrium (LD), and haplotype analysis. LOC_Os10g20160 (SD-RLK-45) showed outstanding characteristics in quantitative real-time PCR (qRT-PCR) analysis in leaf development period, belongs to S-domain receptor-like protein kinases gene and probably to be a main gene regulating flag leaf width of japonica rice. The results of this study provide valuable resources for mining the main genes/QTLs of japonica rice leaf development and molecular breeding of japonica rice ideal leaf shape.

Genetic Variability Studies for Yield and Yield Related Attributes in Rice (Oryza sativa L.) Genotypes

A set of twenty four rice genotypes including one check variety were grown to estimate study genetic variability, heritability, genetic advance, correlation and path coefficient for 13 quantitative characters, observation recorded to study the genetic variability parameters, correlation coefficient and path coefficient for yield and its attributing traits. High to moderate estimates of GCV and PCV were recorded for test weight followed by spikelets per panicle, grain yield per plant, flag leaf width, flag leaf length, tillers per hill, biological yield and panicles per hill. Grain yield indicated significant positive correlation with plant height followed by tillers per hill, panicles per hill, biological yield and harvest index in terms of phenotypic correlation coefficient whereas in terms of genotypic coefficient it showed positive and significant correlation with plant height, tillers per hill, panicles per hill, biological yield and harvest index. Path coefficient analysis showed positive significant direct effects on grain yield per hill were exhibited by plant height, tillers per hill and harvest index at genotypic level whereas it showed positive and significant direct effect for tillers per hill, flag leaf width, biological yield and harvest index at phenotypic level. Thus, these traits are identified as the efficient and potential for indirect selection for the improvement of rice productivity in the present experimental materials.

Variability, Heritability and Genetic advance of introduced upland rice genotypes at Fogera in North Western Ethiopia

Variability, heritability and genetic advance are basic in order to provide information for plant breeding programs. Forty nine upland rice genotypes were tested in 7*7 simple lattice design at Fogera in Wereta station of Adet Agricultural Research Center in 2012/13. The objectives of the study were to estimate the genetic variability, heritability and genetic advance of the genotypes tested. Analysis of variance revealed that there was highly significant difference among the 49 genotypes for all the characters studied. Accessions IR 78937-B-3-B-B-1 and IR 78937-B-3-B-B-2 had the highest yield with a score of 5374.5 kg/ha and 5305.6 kg/ha respectively. The high yielding genotype IR 78937-B-3-B-B-1 had a yield advantage of 57% and 22.2%, respectively, as compared to standard checks Nerica-4 and Hidasie. Phenotypic coefficient of variation (PCV) values ranged from 2.5% for panicle length to 49.98% for number of spikelet per panicle. While the genotypic coefficient of variation (GCV) ranged from 2.4 % for panicle length to 47.6 % for number of spikelet per panicle. Number of tiller per plant (22.47%), number spikelet per panicle (49.98%), thousand seed weight (25.56%) and yield (23.93%) had higher PCV values. The PCV values for flag leaf length (14.79%), flag leaf width (16.12%), and culm length (16.42%) and number of panicle per plant (16.32%) were medium. Flowering cycle (7.81%), maturation cycle (2.9%), and panicle length (2.5%) had lower PCV values. GCV values were low for flowering cycle (7.21%), maturation cycle (1.82%) and panicle length (2.4%); medium for flag leaf length (14.26%), flag leaf width (15.39%), culm length (15.19 %) and number of panicle per plant (15.72%); high for number of tillers per plant (22.18 %), yield (23.07%), thousand seed weight (25.18%) and number of spikelet per panicle (47.60%). The high GCV values of these characters suggest that genetic impact is higher and environmental influence is lower. This study generally had indicated that there was significant genetic variability or divergence among the genotypes. Thus, the improvement program of the upland rice genotypes through direct selection rather than a lengthy crossing program is recommended.

How much the response of rice genotypes to water deficit at the reproductive phase is dependent from environmental conditions?

Rice crop is known as particularly sensitive to water deficit, especially during the reproductive phase when growth of vegetative organs and formation of spikelets are simultaneous. Many works have focused on the response of rice plants to water deficits varying in timing, duration and intensity. Oppositely, the impact of the environmental conditions on the response to a given water deficit remains largely unknown. In order to test it, two experiments under contrasted conditions of temperature, radiation and VPD were conducted on six genotypes in greenhouse in Brazil (S) and in growth chamber in France (GC). The plants were submitted to the same mild water deficit at the reproductive phase, by adjusting FTSW at 0.4. Under irrigation, plant growth rate was reduced and crop duration extended in GC in relation to S: ultimately, this trade-off resulted in similar plant height and biomass in both environments. Under water deficit and in both environments, elongation rate decreased and was associated with an increase in soluble sugars in stem and flag leaf, while starch was reduced in S and negligible in GC because of the low radiation. This common biochemical response displayed a large gradient of values across environments and genotypes, but differentially impacted the branch and spikelet formation on the developing panicle: in carbon limiting conditions (GC), the increase in soluble sugars was associated with the reduction in branch and spikelet number, and conversely in S. At the morphological level, the maintenance of spikelet number on the panicle was correlated with the maintenance of flag leaf width in all genotypes and conditions, that was discussed according to the maintenance of the apical meristem size. Genotypes were discriminated and the study underlined the global tolerance of Cirad 409 and sensitivity of IAC 25.

Studies on Heterosis, Residual Heterosis and Inbreeding Depression for Yield and Related Traits in Sorghum (Sorghum bicolor L.)

Background: Selection of genotypically superior parents is most challenging task for the development of potential hybrids. In conventional plant breeding, magnitude of heterosis and inbreeding depression has been proved very effective in identifying vigorous parental combinations. Methods: The present investigation was carried out to study the heterosis, residual heterosis and inbreeding depression of forty sorghum crosses (F1s and F2s) obtained by crossing of eight restorer lines with five cytoplasmic male sterile lines in Line x Tester mating design in 2013 and 2014. Observations were recorded on morphological traits viz. days to 50% flowering, days to maturity, plant height, flag leaf length, flag leaf width, panicle length, panicle width, panicle weight,1000 seed weight and grain yield per plant. Result: Among all crosses, ICSA467 x UPC2 and MR750A2 x UPC2 were found to be best for most of the characters. Inbreeding depression was recorded as significantly positive for plant height for most of the crosses indicates the occurrence of transgressive segregants in F2 generation.

A Novel QTL Controlling Flag Leaf Width Located on Chromosome Arm 7AS in Bread Wheat (Triticum Aestivum L.)

Background: Wheat is an important cereal crop and improving wheat production is essential for meeting the food demand from the growing population worldwide. Flag leaf width (FLW) is an important trait affecting plant architecture and contributing to grain yield. To detect loci conferring FLW, we assessed a population of recombinant inbred lines (RILs) from a cross of EGA Wylie/Sumai 3 in different environments.Results: A total of six QTL were detected from the population. Two of them located on chromosome 2B and the other four located on chromosomes 2D, 4B, 7A, and 7B, respectively. The percentage of phenotypic variation (PEV) explained by these loci ranged from 14.6% to 33.8%, with LOD scores varying from 3.01 to 7.81. Of them, the locus located on chromosome arm 7AS is likely novel. Significant effects of this locus were detected in multiple trials conducted and the PEV explained by this QTL varied from 14.6% to 19.8% among the different trials. An orthologous analysis based on rice and Arabidopsis identified 3 putative genes underlying this potentially novel locus.Conclusion: This study identified a stable potentially novel QTL in multiple environments and predicted three candidate genes of it, which laid the foundation for further fine-mapping and cloning the gene(s) underlying QFlw.WS-7A with the contribution to grain yield.

Inheritance of some flag leaf and yield characteristics by half-diallel analysis in rice crops (Oryza Sativa L.)

This study was conducted during 2018 and 2019 at the Rice Research and Training Centre farm, Sakha, Kafr el Sheikh, Egypt. Six genotypes of rice, Sakha 101, Giza 178, Irat 170, Wab-56-104, IR65500-127 and IR69853 were half-diallel crossed to estimate the combining ability effect as well as sink and yield potential in rice. Sink capacity (number of spikelets/panicle and 1000-grain weight), source leaf (flag leaf length, flag leaf width and flag leaf area), source-sink association (number of spikelets/panicle to flag leaf area ratio) and traits of yield components (filled grains number/panicle and panicle number) plant and grain yield/plant) were analysed. The results indicated that both general and specific combining ability were highly significant for all the studied characteristics. IR65500-127, Giza 178, and Sakha 101 were identified as good parents, so these parents were suggested for a further recombinant breeding programme. The cross of 3 × 5 was found to be superior for flag leaf width and grain yield, while the cross of 1 × 4 was found to be superior for flag leaf length, flag leaf length/width ratio, chlorophyll content and number of panicles/plant. Advancing these crosses and effected selections in segregating generation would be helpful to develop high yielding varieties. The genetic parameter showed a dominant deviation in one direction was controlled for all characters except flag leaf length. The analysis of the regression line showed that the over-dominance played an important role in the inheritance of gene action for grain yield/plant.

QTL Mapping of Novel Genomic Regions for Yield Related Traits in Doubled Haploid (DH) Population Derived from the Popular Rice Hybrid KRH-2

Background: Rice, being the principal food crop and major nutritional source for more than half of the global population, is also an important source of livelihood in many South and South-East Asian countries. Amidst diminishing natural resources and many biotic-abiotic stresses, increasing the yield of rice varieties remains a challenging task. Identification of novel and yield augmenting alleles from stable rice hybrids is crucial to facilitate their marker-assisted transfer into various genetic backgrounds. Results: Quantitative trait loci (QTL) mapping using a population of 125 doubled haploid (DH) lines developed from the cross IR58025A/KMR3R and 126 polymorphic SSR; EST-derived SSR markers led to the identification of 12 each of major-minor effect QTLs for yield related traits. Major effect QTLs were detected for traits namely days to fifty percent flowering, test (1,000) grain weight, plant height, panicle weight, panicle length, flag leaf width, flag leaf length, biomass and total grain yield/plant explaining the phenotypic variability in the range of 29.95%-56.75%. QTL hotspots were detected on chromosome 3 for the traits, panicle length and total grain yield/plant and on chromosome 6 for the traits, panicle length, flag leaf length and total grain yield/plant. Though many of these QTLs were noted to co-localize with the QTL regions reported in earlier studies, five novel and major effect QTLs for panicle length, biomass, flag leaf width, panicle weight, plant height and three novel minor effect QTLs for panicle weight and fertile grains per panicle, were identified in this study. Conclusions: Through this study, both major-minor effect novel QTLs for crucial yield related traits, viz., fertile grains per panicle, panicle length, panicle weight were identified. Further, the QTL hotspots identified on two different chromosomes for flag leaf length, panicle length and total grain yield/plant shall not only help in understanding the underlying genetic mechanisms of yield regulation but also would provide an insight into the genetic synchrony among the various yield related traits in contributing for yield heterosis. The identified QTL hotspots after their validation can be deployed in breeding programs targeted towards improvement of yield heterosis.

Genotypic response to water deficit applied at reproductive stage in rice: is the response unique across two contrasted climates?

Background: Rice crop is known as very sensitive to water deficit, especially during the reproductive phase when growth of vegetative organs and formation of spikelets are concomitant. The present study questioned whether the maintenance of vegetative organ expansion during a water deficit at the reproductive phase affects the reproductive structure organogenesis, and if relevant traits for adaptation can be identified. To answer these queries, the response to a same reproductive water deficit of six contrasted japonica genotypes has been analyzed under two contrasted climates differing in incident radiation, air hygrometry and temperature (greenhouse in Brazil, Sitis, and growth chamber in France, GC).Results: Under irrigation, plant growth rate was reduced in GC while crop duration was extended: the trade-offs resulted in similar plant height and biomass. From a method able to determine a posteriori the date of panicle initiation (PI), elementary processes were positioned in time, allowing to evaluate how much each process was affected, despite the diversity in phenology across genotypes. Elongation rate decreased with water deficit and was highly associated with an increase in soluble sugars in stem and flag leaf in both experiments, while starch was reduced in Sitis and negligible in GC. This unique response, however, induced a different effect across experiments on branch and spikelet formation. In short, in both experiments, maintenance of spikelet number was highly associated with maintenance of flag leaf and internode width. All variables, including branch and spikelet number, were highly affected with IAC 25 in both experiments, while variations were non-significant with Cirad 409. In addition, some other genotypes expressed a differential response between Sitis and GC, conveying a specific sensitivity to low radiation or to high air temperature. Conclusions: This study highlighted the importance of finely mapping in time elementary growth processes, thanks to PI date determination, in order to detect key traits of adaptation to abiotic stress through phenotyping across genotypes of diverse phenology. The maintenance of flag leaf width or internode diameter under a mild water deficit was highlighted here as a trait associated with the maintenance of yield components.