A Hybrid Rice Optimization Algorithm with Ant System for Feature Selection

This study attempted to characterize the cytoplasmic types of three sterile lines and three maintainer lines of sugar beet, as well as the composition of the Rf1 and Rf2 fertility genes, utilizing molecular markers. Male sterile cytoplasm (S) and normal cytoplasm (N) in sugar beet were identified by polymorphisms in the variable number of tandem repeats (VNTR) locus. Molecular markers s17 and o7 were used to identify the composition of Rf1 and Rf2 fertility genes. In addition, the other four pairs of primers (4E2M15S, 5E3M5S, 1E8M7O and 11E8M4S), which were designed on the basis of genomic and transcriptomic sequences, were selected to identify male sterile and maintainer lines. The amplification bands of VNTR primers demonstrated that the cytoplasmic type of maintainer and sterile lines was N-type and S-type, respectively. The observed segregation of s17 did not significantly difference (p = 1) among three maintainer lines, while significant difference (p < 0.01) was found among three sterile lines. Among four pairs of genomic and transcriptomic primers, only 11E8M4S was observed to distinguish between sterile and maintainer lines of sugar beet. In conclusion, VNTR primers have a high accuracy for identifying the cytoplasmic type of maintainer and sterile lines. s17 and 11E8M4S were also effective for DNA marker-assisted selection of sterile and maintainer lines in sugar beet. However, o7 was not significantly correlated with the fertility of sterile and maintainer lines, suggesting that the Rf2 site may play a little role in the restored fertility of sugar beet.

Aims: The present investigation aimed to assess maintainer and restorer lines independently to identify genetically diverse lines within each group. These selected lines can be used in hybridization and subsequent inbreeding programs to develop superior inbred lines with enhanced seed yield and oil content, based on twelve yield and yield-associated traits. Study Design: Augmented RCBD with 12 blocks was followed. Place and Duration of Study: The experiment was conducted during late Rabi- 2022 at AICRP on Sunflower, ZARS, University of Agricultural Sciences, GKVK, Bangalore. Methodology: A total of of 121 maintainer lines and 17 restorer lines along with 5 checks (CMS-17B, CMS-234B, ARM 243B, RHA-6D-1 and RHA-1-1) were evaluated for 12 yield and yield related traits. Diversity was analyzed using K means clustering. Results: The diversity analysis of maintainer lines resulted in 12 clusters, of which the maximum inter-cluster distance (27.22) was observed between cluster VI and cluster IX. Maintainer lines from these can be improved through hybridization followed by inbreeding and selection. maintainer lines in Cluster II were found to be high seed (mean value of 41.37g per plant) and oil yielders (mean value of 13.43 g per plant). Restorer lines formed five clusters, of which, the maximum inter-cluster distance of 18.29 was observed between cluster II and cluster V indicating that the restorer lines between these clusters are highly divergent. Restorer lines in Cluster II were high seed (mean value of 25.75 g per plant) and oil yielders (mean value of 10.04 g per plant). Conclusion: Overall, the findings indicate that the experimental material possesses substantial genetic diversity, which can be effectively utilized in future crop improvement programs.

Sugar beet is an economically significant crop, and the homozygosity of paired monogerm cytoplasmic male sterile (CMS) and maintainer lines directly influences the number of hybrid combinations that can be created. This study aimed to evaluate the genetic variation within monogerm sugar beet germplasm resources to establish a foundation for advancements in sugar beet breeding and the development of hybrid female parent lines. This study analyzed the genetic diversity of 86 distinct monogerm germplasm resources, including 38 paired monogerm CMS and maintainer lines, 5 individual maintainer lines, and 5 externally introduced sterile lines. The analysis employed 26 pairs of SSR primers and 35 pairs of InDel primers across nine sugar beet chromosomes. Several genetic parameters, and analyses such as structural analysis, genetic diversity analysis, and principal coordinate analysis, were used to evaluate the samples. The results indicated that these strains could be classified into two groups: Group I and Group II. Group I was further divided into three subgroups. Further, 18 pairs of original CMS and maintainer lines were successfully clustered, confirming that their nuclei had achieved homozygosity, making them suitable for use in the development of binary sterile lines. However, 20 other pairs still require further backcrossing to achieve homozygosity. The analysis of molecular variance (AMOVA) revealed that most of the genetic variation occurred within individuals, with relatively low genetic differentiation between groups. Significant genetic differentiation was observed between Subgroups 2 and 3, and between Subgroups 1 and 3. The results suggest that additional monogerm sterile and maintainer lines from these subgroups should be selected to configure binary sterile lines. This study offers a theoretical foundation for developing new sugar beet germplasm resources and cultivating hybrid mother plants.

Thermal Resistance of Common Rice Maintainer and Restorer Lines to High Temperature During Flowering and Early Grain Filling Stages

Fusarium head blight (FHB, caused by Fusarium graminearum) is a severe disease which threatens the yield and quality of harvested grain products, and hence causes major economic losses in wheat (Triticum spp.) and other small grain cereals. One of the infection routes for the pathogen is believed to be through the extruded anther. In order to study the role of the anther on FHB infection, FHB resistance was measured among wheat (Triticum aestivum L.) cultivars with non-extruded infertile anthers in cytoplasmic male sterile (CMS) lines and with extruded fertile anthers in their alloplasmic maintainer lines, and in an unrelated restorer line. We artificially inoculated the lines with F. graminearum (isolate NE 90) at 1.0 × 105 or 2.0 × 105 spores mL−1 for 72 or 96 hours. The results indicated that CMS cultivars were significantly more resistant than the maintainer and restorer cultivars. As the CMS lines differed from the maintainer lines by cytoplasm, anther health, anther extrusion, and seed set, additional experiments are needed to determine the role of each factor in infection. However, this research indicates that fertile anthers most likely are an important part of the infection pathway and of susceptibility to FHB.

An experiment was conducted at Bangladesh Rice Research Institute (BRRI), Gazipur during T.Aman season of 2007 with a view to evaluating seven maintainer and 30 restorer lines for yield and yield contributing characters for selecting promising maintainer and restorer lines for developing rice hybrids in our local environment. Significant variations were noticed among the parental lines for all the characters studied. The CMS lines Gan46A and BRRI9A could be used as female parents in hybrid seed production due to good yield and yield contributing characters recorded in their corresponding maintainer lines. Restorer line BR168R could offer high yield potentiality in heterosis breeding due to its superior yield contributing characters in local environment. DOI: http://dx.doi.org/10.3329/bjar.v38i4.18868 Bangladesh J. Agril. Res. 38(4): 553-562, December 2013

The tms5 mutation exists in most current thermo-sensitive genic male sterility lines, which are essential in hybrid rice production. The Cao group has made an exciting new discovery: TMS5, as a phosphatase, removes 2′,3′-cyclic phosphate (cP) from cP-ΔCCA-tRNAs, enabling efficient tRNA repair. First observed in 1763, 1 male sterility includes cytoplasmic male sterility (CMS) and genic male sterility (GMS). CMS is influenced by both mitochondrial and nuclear genes, while GMS is caused by nuclear genes alone. 2 Hybrid vigor enables heterozygous first filial generation to display better performance for a trait than both parents. 3 Hybrid vigor in rice was observed in 1926; however, hybrid rice breeding was hardly achieved until the widespread application of male sterile lines in 1970s. 4,5 The three-line system, underpinned by CMS-based hybrid seed production, involves three breeding lines: the CMS line, the maintainer line, and the restorer line. In contrast, the two-line system capitalizes on environment-sensitive GMS whose fertility changes in response to environmental factors like day length and temperature. 5 Hybrid rice, which accounts for ~55% of China's rice cultivation area, has led to an over 20% increase in yield. 6 Of this, two-line hybrid rice constitutes ~50%. 7 A mutation in the THERMO-SENSITIVE GENIC MALE STERILE 5 (TMS5) gene, causing the thermos-sensitive genic male sterility (TGMS) trait in the Zhu1S line, is present in >95% of the TGMSbased two-line hybrid rice cultivated in China. 8 Previous studies revealed that TMS5 encodes RNase Z S1 , which cleaves the mRNAs of three ubiquitin fusion ribosomal protein L40 (Ub L40 ) genes into fragments. The overaccumulation of Ub L40 mRNAs, resulting from the tms5 mutation and high temperature, hinders pollen production, leading to male sterility. 9 However, the molecular mechanism underlying tms5-mediated TGMS requires further exploration. In a recent study published in Cell Research, Yan et al. 10 reported that TMS5 functions as a tRNA 2′,3′-cyclic phosphatase, removing 2′,3′-cyclic phosphate (cP) from cP-ΔCCA-tRNAs for efficient tRNA repair (Fig. 1 ). At permissive temperatures, overexpression of tRNA-Ala or the elimination of cP-ΔCCA-tRNA restores the fertility of the tms5 mutant. Inspired by the biochemical function of TMS5 homologs in humans, the authors verified that both recombinant and endogenous TMS5 removed cP from cP-ΔCCA-tRNA, allowing TRNT1 to mediate CCA addition and mature tRNA recycling. Crystallographic analysis uncovered that TMS5 forms an antiparallel dimer, with its active site providing a pseudo-octahedral coordination crucial for dual zinc ion binding and enzymatic

Cytoplasmic male sterility (CMS), which is a maternally inherited trait and controlled by novel chimeric genes in the mitochondrial genome, plays a pivotal role in the production of hybrid seed. In cotton, no PCR-based marker has been developed to discriminate CMS-D8 (from Gossypium trilobum) from its normal Upland cotton (AD1, Gossypium hirsutum) cytoplasm. The objective of the current study was to develop PCR-based single nucleotide polymorphic (SNP) markers from mitochondrial genes for the CMS-D8 cytoplasm. DNA sequence variation in mitochondrial genes involved in the oxidative phosphorylation chain including ATP synthase subunit 1, 4, 6, 8 and 9, and cytochrome c oxidase 1, 2 and 3 subunits were identified by comparing CMS-D8, its isogenic maintainer and restorer lines on the same nuclear genetic background. An allelic specific PCR (AS-PCR) was utilized for SNP typing by incorporating artificial mismatched nucleotides into the third or fourth base from the 3' terminus in both the specific and nonspecific primers. The result indicated that the method modifying allele-specific primers was successful in obtaining eight SNP markers out of eight SNPs using eight primer pairs to discriminate two alleles between AD1 and CMS-D8 cytoplasms. Two of the SNPs for atp1 and cox1 could also be used in combination to discriminate between CMS-D8 and CMS-D2 cytoplasms. Additionally, a PCR-based marker from a nine nucleotide insertion-deletion (InDel) sequence (AATTGTTTT) at the 59-67 bp positions from the start codon of atp6, which is present in the CMS and restorer lines with the D8 cytoplasm but absent in the maintainer line with the AD1 cytoplasm, was also developed. A SNP marker for two nucleotide substitutions (AA in AD1 cytoplasm to CT in CMS-D8 cytoplasm) in the intron (1,506 bp) of cox2 gene was also developed. These PCR-based SNP markers should be useful in discriminating CMS-D8 and AD1 cytoplasms, or those with CMS-D2 cytoplasm as a rapid, simple, inexpensive, and reliable genotyping tool to assist hybrid cotton breeding.

A hybrid algorithm using ant and bee colony optimization for feature selection and classification (AC-ABC Hybrid)

An enhanced ACO algorithm to select features for text categorization and its parallelization

Hybrid rice technology is aneffective way for increasing rice production to meet the future rice demands of growing population. Inadequate numbers of restorer and maintainer lines are the major constrains for the development of location-specific rice hybrids. Present investigation involves the identification of restorers and maintainers for tarai regions of Uttar Pradesh and Uttarakhand. Under this study, three cytoplasmic male sterile (CMS) lines and 43 elite rice genotypes from diverse source of origin were crossed in line × tester fashion and test crosses were evaluated in order to identify potential restorers and maintainers. Genotypes were categorized as restorers (> 80% spikelet fertility), partial restorers (20 to 79% spikelet fertility), partial maintainers (10–20% spikelet fertility) and maintainers (< 10% spikelet fertility). The F1’s expressed different fertility reactions with different CMS lines of the same cytoplasmic source. Out of 45 male lines UPR 3764-5-13 and UPR 3744-7-1-1 behaved as maintainer with two CMS lines and IR 09N522 and CT 19533-3-4-2-2P-2P found restorer with all the CMS lines. The identified maintainers and restorers can play a pivotal role in hybrid rice development.

BackgroundThe mitochondrial genomes of higher plants vary remarkably in size, structure and sequence content, as demonstrated by the accumulation and activity of repetitive DNA sequences. Incompatibility between mitochondrial genome and nuclear genome leads to non-functional male reproductive organs and results in cytoplasmic male sterility (CMS). CMS has been used to produce F1 hybrid seeds in a variety of plant species.ResultsHere we compared the mitochondrial genomes (mitogenomes) of Gossypium hirsutum sterile male lines CMS-2074A and CMS-2074S, as well as their restorer and maintainer lines. First, we noticed the mitogenome organization and sequences were conserved in these lines. Second, we discovered the mitogenomes of 2074A and 2074S underwent large-scale substitutions and rearrangements. Actually, there were five and six unique chimeric open reading frames (ORFs) in 2074A and 2074S, respectively, which were derived from the recombination between unique repetitive sequences and nearby functional genes. Third, we found out four chimeric ORFs that were differentially transcribed in sterile line (2074A) and fertile-restored line.ConclusionsThese four novel and recombinant ORFs are potential candidates that confer CMS character in 2074A. In addition, our observations suggest that CMS in cotton is associated with the accelerated rates of rearrangement, and that novel expression products are derived from recombinant ORFs.

High-dimensional datasets (HDDs) pose significant challenges in feature selection due to their complex nature. While metaheuristic algorithms like the Whale Optimisation Algorithm (WOA) have shown promise in addressing these challenges, stability issues are least addressed. Through an extensive literature review, it was identified that stability is manifested in the equilibrium of exploration and exploitation. Hence, this study introduced the Hierarchical Whale Optimisation Algorithm (HiWOA), an approach designed to enhance the WOA’s stability and performance in HDD feature selection tasks. The HiWOA incorporates a two-phase strategy comprising a nonlinear control parameter based on the arcsine function and a hierarchical position-update mechanism adapted from the Grey Wolf Optimiser. The proposed HiWOA was evaluated through 23 benchmark optimisation functions and feature selection experiments on 11 medical HDDs. The results indicate that the HiWOA outperformed the WOA and a modified variant (mWOA) in terms of a better fitness value, a more balanced exploration-exploitation ratio, and improved classification accuracy with fewer selected features. These findings demonstrate the HiWOA’s effectiveness in enhancing stability, making it a robust solution for high-dimensional optimisation and feature selection.

Chapter 14 - Review on hybrid feature selection and classification of microarray gene expression data

Significant heterosis for seed yield in oilseed rape has created interest in the development of hybrid cultivars. The DNA‐based marker protocol, sequence‐related amplified polymorphism (SRAP) was used to determine genetic diversity among oilseed rape maintainer and restorer lines. This measure was used in an attempt to establish an association between genetic distance and heterosis in hybrids for various agronomic traits. A total of 118 polymorphic loci were generated by 18 SRAP primer combinations. Based on the polymorphism generated by the markers, calculated similarity index values ranged from 0.46 to 0.97. Cluster analysis grouped 10 maintainer and 12 restorer lines into three groups, with the exception of two maintainer lines, PM5 and PM9, which fell outside these groups. The grouping of the lines was largely in agreement with the available pedigree data on their origin and agronomic performance. Analysis of variance among inbred lines and their resulting F1 hybrids over two locations revealed significant differences for plant height, days to maturity and seed yield, but not for oil content. Substantial mid‐parent heterosis was observed only for seed yield, and ranged from 26% to 169%. All hybrids surpassed their respective inbred lines for this trait, except for a single cross combination of related lines. In general, crosses of lines located in different clusters yielded more than those from the same clusters. Regression analysis revealed a statistically significant relationship between the genetic distance of the parents and seed yield in their hybrid, and their derived mid‐parent and high‐parent heterosis. The correlation coefficient between genetic distance and yield (0.64) indicated a moderately strong relationship, so it is possible that some of the SRAP markers might be linked to quantitative trait loci for seed yield.