Genetic Yield Improvement Research Articles

Genomic selection shows improved expected genetic gain over phenotypic selection of agronomic traits in allotetraploid white clover

Key messageGenomic selection using white clover multi-year-multi-site data showed predicted genetic gains through integrating among-half-sibling-family phenotypic selection and within-family genomic selection were up to 89% greater than half-sibling-family phenotypic selection alone.Genomic selection, an effective breeding tool used widely in plants and animals for improving low-heritability traits, has only recently been applied to forages. We explored the feasibility of implementing genomic selection in white clover (Trifolium repens L.), a key forage legume which has shown limited genetic improvement in dry matter yield (DMY) and persistence traits. We used data from a training population comprising 200 half-sibling (HS) families evaluated in a cattle-grazed field trial across three years and two locations. Combining phenotype and genotyping-by-sequencing (GBS) data, we assessed different two-stage genomic prediction models, including KGD-GBLUP developed for low-depth GBS data, on DMY, growth score, leaf size and stolon traits. Predictive abilities were similar among the models, ranging from −0.17 to 0.44 across traits, and remained stable for most traits when reducing model input to 100–120 HS families and 5500 markers, suggesting genomic selection is viable with fewer resources. Incorporating a correlated trait with a primary trait in multi-trait prediction models increased predictive ability by 28–124%. Deterministic modelling showed integrating among-HS-family phenotypic selection and within-family genomic selection at different selection pressures estimated up to 89% DMY genetic gain compared to phenotypic selection alone, despite a modest predictive ability of 0.3. This study demonstrates the potential benefits of combining genomic and phenotypic selection to boost genetic gains in white clover. Using cost-effective GBS paired with a prediction model optimized for low read-depth data, the approach can achieve prediction accuracies comparable to traditional models, providing a viable path for implementing genomic selection in white clover.

A novel transcription factor OsMYB73 affects grain size and chalkiness by regulating endosperm storage substances' accumulation-mediated auxin biosynthesis signalling pathway in rice.

Enhanced grain yield and quality traits are everlasting breeding goals. It is therefore of great significance to uncover more genetic resources associated with these two important agronomic traits. Plant MYB family transcription factors play important regulatory roles in diverse biological processes. However, studies on genetic functions of MYB in rice yield and quality are rarely to be reported. Here, we investigated a nucleus-localized transcription factor OsMYB73 which is preferentially expressed in the early developing pericarp and endosperm. We generated targeted mutagenesis of OsMYB73 in rice, and the mutants had longer grains with obvious white-belly chalky endosperm appearance phenotype. The mutants displayed various changes in starch physicochemical characteristics and lipid components. Transcriptome sequencing analysis showed that OsMYB73 was chiefly involved in cell wall development and starch metabolism. OsMYB73 mutation affects the expression of genes related to grain size, starch and lipid biosynthesis and auxin biosynthesis. Moreover, inactivation of OsMYB73 triggers broad changes in secondary metabolites. We speculate that rice OsMYB73 and OsNF-YB1 play synergistic pivotal role in simultaneously as transcription activators to regulate grain filling and storage compounds accumulation to affect endosperm development and grain chalkiness through binding OsISA2, OsLTPL36 and OsYUC11. The study provides important germplasm resources and theoretical basis for genetic improvement of rice yield and quality. In addition, we enriches the potential biological functions of rice MYB family transcription factors.

A molecular module improves rice grain quality and yield at high temperatures.

Excessive temperatures during grain filling can compromise endosperm starch biosynthesis and decrease grain quality and yield in rice. However, the molecular mechanisms underlying these remain unclear. Here, we show that heat shock protein OsHsp40-1 interacts with and elevates the ATPase activity of OsHsp70-2 in rice. OsHsp40-1 also interacts with the key starch biosynthetic enzymes OsGBSSI and OsPPDKB and thereby enhances their stability and activity, which is essential for maintaining rice quality and grain yield under moderate high-temperature (HT) conditions. Overexpression of OsHsp70-2 and OsHsp40-1 in rice significantly improved grain quality and yield at HT. Furthermore, a haplotype analysis identified favorable alleles of OsHsp70-2 and OsHsp40-1, which could be used for improving thermotolerance in rice. Collectively, our findings reveal a novel mechanism by which the OsHsp70-2-OsHsp40-1 module ameliorates the effects of HT on starch biosynthesis, providing a new strategy for genetic improvement of rice quality and yield under HT conditions.

Overexpression of vacuolar H+-pyrophosphatase from a recretohalophyte Reaumuria trigyna enhances vegetative growth and salt tolerance in transgenic Arabidopsis thaliana.

Reaumuria trigyna, a wild and endangered salt-secreting small shrub, is distributed in arid and semi-arid areas of Inner Mongolia, China. An H+-pyrophosphatase gene (RtVP1) was isolated from R. trigyna according to transcriptomic data, which encoded a plasma membrane and tonoplast-localized protein. RtVP1 was quickly upregulated by NaCl and exogenous abscisic acid treatment and rescued the sucrose deficiency sensitive phenotype of the AtVP1 mutant (avp1). Transgenic Arabidopsis overexpressing RtVP1 exhibited a higher leaf area, plant height, fresh weight, root length, and soluble carbohydrate accumulation compared to the wild type (WT) under normal conditions. RtVP1 overexpression increased the seed germination rate and decreased the reduction rate of fresh weight, root length, and chlorophyll content in transgenic plants under salt stress. Catalase enzyme activity, proline content, relative water content, and soluble sugar content were significantly increased in transgenic Arabidopsis under salt stresses, but the malondialdehyde content was dramatically decreased. More K+ and less Na+ were accumulated in transgenic Arabidopsis leaves, resulting in a relatively lower Na+/K+ ratio. In transgenic Arabidopsis roots, K+ was unchanged, but Na+ and the Na+/K+ ratios were reduced compared to those in WT. More Na+ and K+ were accumulated in the intracellular of transgenic yeast, and the Na+/K+ ratio was significantly reduced compared to the control. These results showed that R. trigyna RtVP1 promotes the vegetative growth of plants, mainly by regulating carbohydrate metabolism, and confers salt tolerance in transgenic Arabidopsis by maintaining Na+/K+ homeostasis and enhancing the antioxidant and osmotic regulatory capacity. These results indicated that RtVP1 can serve as an important candidate gene for genetic improvement of crop yield and salt tolerance.

Mining Candidate Genes for Maize Tassel Spindle Length Based on a Genome-Wide Association Analysis.

Maize tassel spindle length is closely related to the number of pollen grains and the duration of the flowering stage, ultimately affecting maize yield and adaptations to stress conditions. In this study, 182 maize inbred lines were included in an association population. A genome-wide association study was conducted on maize tassel spindle length using the Q + K model. With p ≤ 1.0 × 10-4 applied as the significance threshold, 240 SNPs significantly associated with tassel spindle length were detected, which were associated with 99 quantitative trait loci (QTLs), with 21 QTLs detected in two or more environments. Moreover, 51 candidate genes were detected in 21 co-localized QTLs. A KEGG enrichment analysis and candidate gene expression analysis indicated that Zm00001d042312 affects plant hormone signal transduction and is highly expressed in maize tassels. A haplotype analysis of Zm00001d042312 revealed three main haplotypes, with significant differences between Hap1 and Hap2. In conclusion, we propose that Zm00001d042312 is a gene that regulates maize tassel spindle length. This study has further elucidated the genetic basis of maize tassel spindle length, while also providing excellent genetic targets and germplasm resources for the genetic improvement of maize tassel spindle length and yield.

OsGRF6-OsYUCCA1/OsWRKY82 Signaling Cascade Upgrade Grain Yield and Bacterial Blight Resistance in Rice.

As a major crop in the world, the sustainable development of rice is often severely restricted by bacterial blight. Breeding crops with resistance is an efficient way to control bacterial blight. However, enhancing resistance often incurs a fitness penalty, making it challenging to simultaneously increase bacterial blight resistance and yield potential. In this study, it is found that OsGRF6, besides being a high-yield gene, can significantly improve rice bacterial blight resistance. Compared with wild-type, the lesion lengths of transgenic material overexpressing OsGRF6 are significantly reduced after inoculation with Xanthomonas oryzae pv. oryzae (Xoo). Furthermore, OsGRF6 can directly bind to the promoters of OsYUCCA1 and OsWRKY82, upregulating their transcription and thereby increasing rice bacterial blight resistance and yield. Haplotypic analysis based on the promoter and genome sequence combined with evolutionary analysis revealed that OsGRF6 is mainly comprised by the OsGRF6XI and OsGRF6GJ subtypes. The superior haplotype OsGRF6Hap4 increased its transcriptional activity and contributed to bacterial blight resistance and rice yield. Together, this study provides theoretical support for further revealing the synergistic regulatory mechanism and genetic improvement of rice high yield and bacterial blight resistance, offering a new strategy for developing disease-resistant cultivars.

Evaluate the Genetic Divergence and Principal Component Analysis in Bread Wheat (Triticum aestivum L.)

The current investigation was carried out on some bread wheat (Triticum aestivum L.) genotypes throughout spring season to evaluate their heat tolerance via Cluster Analysis and principal component analysis (PCA). The experiment was accomplished in an augmented block design with 60 genotypes and three replications. Evaluations were carried out on 26 quantitative traits. Cluster analysis showed five clusters, cluster I with 56 genotypes and clusters II, III, IV and V with only one genotype each. The clusters II, III, IV and V have only one genotype each, so their intra-cluster distances were zero. The intra-cluster distance for cluster I was 57.879. The maximum and minimum inter cluster distance was found between cluster II and III (267.377) and between cluster I and II (86.469), respectively. Cluster I showed the earliest (76.689 days) average for early maturity (days to 50% heading) and cluster III showed the maximum (27.664) average for grain yield (grain yield per plant). PCA indicated that the five principal components (PC1 to PC5) accounted for 65.61% of the total variance. PC1 accounted for 11.51% of the total variance and showed positive factor loading for almost traits. Harvest index, grain yield per plant, flag leaf width and leaf rolling showed the highest factor loadings for PC1. As a result of the foregoing data and analysis, it is possible to conclude that there is great potential for effective genetic improvement for grain yield and correlated traits in the present wheat genotypes.

Marker assisted identification of improved restorer lines with yield enhancing genes adaptable for aerobic conditions

To feed the world's growing population, development and introduction of climate resilient rice varieties/hybrids with increased yield ability are the need of the hour. This can be accomplished through novel genetic approaches such as hybrid rice technology, using a diverse set of parental lines with high restoring ability and specific desirable traits. In our study, for perse genetic yield improvement in aerobic restorer line AR 9-18R, hybridization was carried out with yield enhancing donor YPK 198 possessing Gn1a and OsSPL14 during kharif, 2018 and generated F1s were fixed for its hybridity through morphological and molecular analysis. In kharif, 2019 two hundred and five F2 population obtained were screened for two yield-enhancing Gn1a and OsSPL14 genes along with two fertility restorer genes Rf3 and Rf4 at ICAR-IIRR, Hyderabad. c2 analysis revealed that the c2 value of both yield enhancing genes was non-significant as the population was segregated in a ratio of 1:2:1. whereas c2 value for fertility restorer genes was significant as population deviated from 1:2:1. Phenotypic evaluation of F2 population for yield related traits exhibited high GCV and PCV for number of productive tillers, number of grains per panicle and single plant yield. Plant height, number of productive tillers, number of grains per panicle and single plant yield displayed high heritability along with high genetic advance as per cent of mean. Correlation and path co-efficient analysis revealed that plant height, number of productive tillers and number of grains per panicle are very important traits as selection criteria for effective yield improvement.

Cobalt 60 (60Co) Gamma Ray Irradiation for Genetic Improvement of Edamame Plant Growth and Yield (Glycine max. (L) Merril) M2 Generation

Cobalt 60 (60Co) Gamma Ray Irradiation for Genetic Improvement of Edamame Plant Growth and Yield (Glycine max. (L) Merril) M2 Generation

Transcription factor ZmDof22 enhances drought tolerance by regulating stomatal movement and antioxidant enzymes activities in maize (Zea mays L.).

The Dof22 gene encoding a deoxyribonucleic acid binding with one finger in maize, which is associated with its drought tolerance. The identification of drought stress regulatory genes is essential for the genetic improvement of maize yield. Deoxyribonucleic acid binding with one finger (Dof), a plant-specific transcription factor family, is involved in signal transduction, morphogenesis, and environmental stress responses. In present study, by weighted correlation network analysis (WGCNA) and gene co-expression network analysis, 15 putative Dof genes were identified from maize that respond to drought and rewatering. A real-time fluorescence quantitative PCR showed that these 15 genes were strongly induced by drought and ABA treatment, and among them ZmDof22 was highly induced by drought and ABA treatment. Its expression level increased by nearly 200 times after drought stress and more than 50 times after ABA treatment. After the normal conditions were restored, the expression levels were nearly 100 times and 40 times of those before treatment, respectively. The Gal4-LexA/UAS system and transcriptional activation analysis indicate that ZmDof22 is a transcriptional activator regulating drought tolerance and recovery ability in maize. Further, overexpressed transgenic and mutant plants of ZmDof22 by CRISPR/Cas9, indicates that the ZmDof22, improves maize drought tolerance by promoting stomatal closure, reduces water loss, and enhances antioxidant enzyme activity by participating in the ABA pathways. Taken together, our findings laid a foundation for further functional studies of the ZmDof gene family and provided insights into the role of the ZmDof22 regulatory network in controlling drought tolerance and recovery ability of maize.

OsLESV and OsESV1 promote transitory and storage starch biosynthesis to determine rice grain quality and yield

Transitory starch is an important carbon source in leaves, and its biosynthesis and metabolism are closely related to grain quality and yield. The molecular mechanisms controlling leaf transitory starch biosynthesis and degradation and their effects on rice (Oryza sativa) quality and yield remain unclear. Here, we show that OsLESV and OsESV1, the rice orthologs of AtLESV and AtESV1, are associated with transitory starch biosynthesis in rice. The total starch and amylose contents in leaves and endosperms are significantly reduced, and the final grain quality and yield are compromised in oslesv and osesv1 single and oslesv esv1 double mutants. Furthermore, we found that OsLESV and OsESV1 bind to starch, and this binding depends on a highly conserved C-terminal tryptophan-rich region that acts as a starch-binding domain. Importantly, OsLESV and OsESV1 also interact with the key enzymes of starch biosynthesis, granule-bound starch synthase I (GBSSI), GBSSII, and pyruvate orthophosphote dikiase (PPDKB), to maintain their protein stability and activity. OsLESV and OsESV1 also facilitate the targeting of GBSSI and GBSSII from plastid stroma to starch granules. Overexpression of GBSSI, GBSSII, and PPDKB can partly rescue the phenotypic defects of the oslesv and osesv1 mutants. Thus, we demonstrate that OsLESV and OsESV1 play a key role in regulating the biosynthesis of both leaf transitory starch and endosperm storage starch in rice. These findings deepen our understanding of the molecular mechanisms underlying transitory starch biosynthesis in rice leaves and reveal how the transitory starch metabolism affects rice grain quality and yield, providing useful information for the genetic improvement of rice grain quality and yield.

Milk Protein Genes Polymorphism in Indigenous and Crossbred Cattle from a private Dairy Farm in Ethiopia

Kappa casein and beta lactoglobulin genes are major milk proteins which have a direct effect on protein content in dairy cattle. Molecular-based selection through the identification of genetic polymorphism of major protein genes can be used to gain genetic improvement of milk protein yield. The objective of this study was to identify kappa casein (CSN3) and beta lactoglobulin (LGB) genes polymorphisms in indigenous and crossbreed cattle. A total of 90 whole blood samples were collected from individual animal in a private dairy farm. DNA extraction and quality assessment were done salting out procedure and gel electrophoresis, respectively. Polymerase chain reaction (PCR) was performed with gene specific primers. For genotyping, PCR products of CSN3 gene was digested with HinfI and HindIII while LGB gene was digested with HaeIII restriction enzymes. Two haplotypes A and B; three genotypes, AA, AB and BB were observed at CSN3 of HinfI site and LGB HaeIII site, but only AA and AB were observed at CSN3 of HindIII site in crossbred and indigenous cattle populations. However, at CSN3 locus, A allele was found to be more common (0.65) in indigenous cattle than the B allele (0.35), while B (0.51) allele and AB genotype (0.81) were more frequent in crossbred cattle. But, LGB B allele was higher in indigenous cattle (0.67) compared to Allele A (0.33). LGB BB genotype (0.57) is higher followed by AA genotype in indigenous cattle while both allele and genotypic frequencies are equal in crossbred cattle. Both CSN3 and LGB loci were polymorphic in studied populations. Expected heterozygosity was higher in crossbred (0.49, 0.50) than in indigenous (0.38, 0.33) cattle at CSN3 and LGB locus, respectively which might be due to breed variation. The current findings showed that both CSN3 and LGB genes could be promising diagnostic markers in selecting dairy cattle breed. However, further investigations with large sample size and association study with milk composition is required to substantiate the current result.

Genome-wide identification of the key kinesin genes during fiber and boll development in upland cotton (Gossypium hirsutum L.).

Kinesin is a kind of motor protein, which interacts with microtubule filaments and regulates cellulose synthesis. Cotton fiber is a natural model for studying the cellular development and cellulose synthesis. Therefore, a systematic research of kinesin gene family in cotton (Gossypium spp.) will be beneficial for both understanding the function of kinesin protein and assisting the fiber improvement. Here, we aimed to identify the key kinesin genes present in cotton by combining genome-wide expression profile data, association mapping, and public quantitative trait loci (QTLs) in upland cotton (G. hirsutum L.). Results showed that 159 kinesin genes, including 15 genes of the kinesin-13 gene subfamily, were identified in upland cotton; of which 157 kinesin genes can be traced back to the diploid ancestors, G. raimondii and G. arboreum. Using a combined analysis of public QTLs and genome-wide expression profile information, there were 29 QTLs co-localized together with 28 kinesin genes in upland cotton, including 10 kinesin-13 subfamily genes. Genome-wide expression profile data indicated that, among the 28 co-localized genes, seven kinesin genes were predominantly expressed in fibers or ovules. By association mapping analysis, 30 kinesin genes were significantly associated with three fiber traits, among which a kinesin-13 gene, Ghir_A11G028430, was found to be associated with both cotton boll length and lint weight, and one kinesin-7 gene, Ghir_D04G017880 (Gh_Kinesin7), was significantly associated with fiber strength. In addition, two missense mutations were identified in the motor domain of the Gh_Kinesin7 protein. Overall, the kinesin gene family seemingly plays an important role in cotton fiber and boll development. The exploited kinesin genes will be beneficial for the genetic improvement of fiber quality and yield.

Genome-wide identification of the key Kinesin genes during fiber and boll development in upland cotton (Gossypium hirsutum L).

Kinesin is a kind of motor protein, which interacts with microtubule filaments and regulates cellulose synthesis. Cotton fiber is a natural model for studying the cellular development and cellulose synthesis. Therefore, a systematic research of Kinesin gene family in cotton (Gossypium spp.) will be beneficial for both understanding the function of Kinesin protein and assisting the fiber improvement. Here, we aimed to identify the key Kinesin genes present in cotton by combining genome-wide expression profile data, association mapping, and public quantitative trait loci (QTLs) in upland cotton (Gossypium hirsutum L.). Results showed that 159 Kinesin genes, including 15 genes of the Kinesin-13 gene subfamily, were identified in upland cotton; of which 157 Kinesin genes can be traced back to the diploid ancestors, G. raimondii and G. arboreum. Using a combined analysis of public QTLs and genome-wide expression profile information, there were 29 QTLs co-localized together with 28 Kinesin genes in upland cotton, including 10 Kinesin-13 subfamily genes. Genome-wide expression profile data indicated that, among the 28 co-localized genes, seven Kinesin genes were predominantly expressed in fibers or ovules. By association mapping analysis, 30 Kinesin genes were significantly associated with three fiber traits, among which a Kinesin-13 gene, Ghir_A11G028430, was found to be associated with both cotton boll length and lint weight, and one Kinesin-7 gene, Ghir_D04G017880 (Gh_Kinesin7), was significantly associated with fiber strength. In addition, two missense mutations were identified in the motor domain of the Gh_Kinesin7 protein. Overall, the Kinesin gene family seemingly plays an important role in cotton fiber and boll development. The exploited Kinesin genes will be beneficial for the genetic improvement of fiber quality and yield.

Integration of transcriptome and DNA methylome analysis reveals the molecular mechanism of taproot yield heterosis in radish (Raphanus sativus L.)

Heterosis, a crucial biological phenomenon, plays a vital role in determining the yield and quality of plants. Radish, an important root vegetable crop, exhibits notable heterosis in terms of root yield and quality. Nevertheless, the specific molecular mechanism behind the formation of heterosis in radish remains unclear. Herein, transcriptome and DNA methylome analyses were performed on F1 hybrids and parental lines. Expression level dominance (ELD) genes and allele-specific expression (ASEG) genes together significantly contribute to heterosis, primarily through energy metabolism and plant hormone signal transduction pathway. Additionally, an increase in the average methylation level in the F1 hybrids was observed compared to the parental lines. Interestingly, a negative correlation was found between the methylation level of differentially expressed genes (DEGs) in gene body regions and their expression levels in NAU-LB and the F1 hybrids. Conversely, a contrasting trend was observed between NAU-YH and the F1 hybrids. Furthermore, when the parental lines and the F1 hybrids were treated with 5-azacytidine, the hybrids were more sensitive to methylation inhibitors than their parents. A significant decrease was observed in root weight and total sugar content in the F1 hybrids compared to the control. Immunolocalization results indicated a significant decrease in the auxin content of the F1 hybrid under 5-azacytidine treatment. Proliferating cell nuclear antigen immunolocalization also revealed significant inhibition of vascular cambium activity in both the hybrids and parental lines. Notably, the expression profiles of a few differentially methylated DEGs including RsSUS1, RsSUC2a, RsIAA7, and RsIAA18, were significantly increased in the root of hybrids compared to their parents, suggesting a potential role for DNA methylation in yield heterosis. Collectively, these findings would provide valuable insight into the molecular mechanism underlying taproot yield heterosis and have the potential to facilitate the genetic improvement of taproot yield and quality in radish breeding programs.

SSR-marker Assisted Evaluation of Genetic Diversity in Greengram [Vigna radiata (L.) Wilcezk

Background: Assessing genetic diversity in greengram is a prerequisite for its genetic improvement for yield and quality. DNA markers such as simple sequence repeats (SSRs) have been preferred in this crop for the analysis of genetic diversity because SSR markers are locus-specific, widely dispersed throughout the genome, highly polymorphic due to variation in repeat units, highly informative because of co-dominant nature, high reproducibility and ease of assay by PCR (Polymerase chain reaction). The current study aimed to study the genetic diversity among the mutants of greengram at the molecular level using SSR markers. Methods: In this study, twenty-five SSR markers were used to analyze the genetic diversity amongst twenty mutant genotypes of greengram along with their parents. Genomic DNA was isolated from the leaves by using the standard CTAB DNA extraction method. Then DNA purification and PCR amplifications were carried out. The genetic variability and diversity among genotypes was examined by assessing the scoring of the amplified bands by SSR -PCR amplification. Result: Seventeen SSR primers generated 102 polymorphic bands with an average of the six polymorphic bands per primer. The number of alleles per locus ranged from four to nine. The size of amplification product varied for each primer and the range found to be 100bp to 2000bp. The mean polymorphic information content (PIC) value for SSR markers was found to be 0.6335. The value of Jaccard’s similarity coefficient had ranged from 0.07-0.70 with an average value of 0.38. The dendrogram constructed on SSR molecular markers data through the unweighted pair group method with arithmetic averages (UPGMA) method had enabled grouping of the genotypes into thirteen clusters. The results indicate the usefulness of SSR markers in the assessment of genetic variability and diversity among the mutant genotypes of greengram.

Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context.

Genomic selection has been utilized for genetic improvement in both plant and animal breeding and is a favorable technique for quantitative trait development. Within this study, genomic selection was evaluated within a breeding program, using novel validation methods in addition to plant materials and data from a commercial soybean (Glycine max) breeding program. A total of 1501 inbred lines were used to test multiple genomic selection models for multiple traits. Validation included cross-validation, inter-environment, and empirical validation. The results indicated that the extended genomic best linear unbiased prediction (EGBLUP) model was the most effective model tested for yield, protein, and oil in cross-validation with accuracies of 0.50, 0.68, and 0.64, respectively. Increasing marker number from 1000 to 3000 to 6000 single nucleotide polymorphism markers leads to statistically significant increases in accuracy. Cross-environment predictions were statistically lower than cross-validation with accuracies of 0.24, 0.54, and 0.42 for yield, protein, and oil, respectively, using the extended genomic BLUP model. Empirical validation, predicting the yield of 510 soybean lines, had a prediction accuracy of 0.34, with the inclusion of a maturity covariate leading to a notable increase in accuracy. Genomic selection identified high-performance lines in inter-environment predictions: 34% of lines within the upper quartile of yield, and 51% and 48% of the highest quartile protein and oil lines, respectively. Statistically similar results occurred comparing rankings in empirical validation and selection for advancements in yield trials. These results indicate that genomic selection is a useful tool for selection decisions.

Novel quantitative trait loci from an interspecific Brassica rapa derivative improve pod shatter resistance in Brassica napus.

Pod shatter is a trait of agricultural relevance that ensures plants dehisce seeds in their native environment and has been subjected to domestication and selection for non-shattering types in several broadacre crops. However, pod shattering causes a significant yield reduction in canola (Brassica napus L.) crops. An interspecific breeding line BC95042 derived from a B. rapa/B. napus cross showed improved pod shatter resistance (up to 12-fold than a shatter-prone B. napus variety). To uncover the genetic basis and improve pod shatter resistance in new varieties, we analysed F2 and F2:3 derived populations from the cross between BC95042 and an advanced breeding line, BC95041, and genotyped with 15,498 DArTseq markers. Through genome scan, interval and inclusive composite interval mapping analyses, we identified seven quantitative trait loci (QTLs) associated with pod rupture energy, a measure for pod shatter resistance or pod strength, and they locate on A02, A03, A05, A09 and C01 chromosomes. Both parental lines contributed alleles for pod shatter resistance. We identified five pairs of significant epistatic QTLs for additive x additive, additive dominance and dominance x dominance interactions between A01/C01, A03/A07, A07/C03, A03/C03, and C01/C02 chromosomes for rupture energy. QTL effects on A03/A07 and A01/C01 were in the repulsion phase. Comparative mapping identified several candidate genes (AG, ABI3, ARF3, BP1, CEL6, FIL, FUL, GA2OX2, IND, LATE, LEUNIG, MAGL15, RPL, QRT2, RGA, SPT and TCP10) underlying main QTL and epistatic QTL interactions for pod shatter resistance. Three QTLs detected on A02, A03, and A09 were near the FUL (FRUITFULL) homologues BnaA03g39820D and BnaA09g05500D. Focusing on the FUL, we investigated putative motifs, sequence variants and the evolutionary rate of its homologues in 373 resequenced B. napus accessions of interest. BnaA09g05500D is subjected to purifying selection as it had a low Ka/Ks ratio compared to other FUL homologues in B. napus. This study provides a valuable resource for genetic improvement for yield through an understanding of the genetic mechanism controlling pod shatter resistance in Brassica species.

Influence of Genetic Variability Parameters, Character Association and Path Analysis for Grain Yield and its Attributing Traits in Kodo Millet Improvement

A set of 64 genotypes of kodo millet comprising of germplasm accessions and released varieties were evaluated for their genetic variability, heritability, genetic advance as per cent of mean, character associations and path coefficients using 11 agro-morphological traits during kharif 2022 in an Alpha Lattice Design with two replications. The analysis of variance revealed the presence of significant variations among the genotypes for all the traits evaluated. High PCV and GCV were observed for the traits viz., plant height, number of tillers, panicle length, peduncle length, thumb length, grain yield, and fodder yield. It indicated the presence of substantial variability and a low environmental influence on these traits. High heritability combined with high genetic advance as per cent of mean (GAM) was observed for plant height, peduncle length, panicle length, and fodder yield, which indicated the predominance of additive gene action and selection based on these traits would be more reliable. Grain yield exhibited significant and positive correlation with days to 50% flowering, number of tillers, panicle length, number of racemes, test weight and fodder yield. Genotypic path analysis revealed that highest direct positive effect on grain yield was exhibited by days to 50% flowering, number of tillers, panicle length, test weight and fodder yield. Hence, the above-mentioned traits exhibiting positive significant correlation and positive direct effect on grain yield could be considered as important traits to be included in the selection criteria to achieve genetic improvement of grain yield in kodo millet.

Mapping of QTLs for Brown Rice Traits Based on Chromosome Segment Substitution Line in Rice (Oryza sativa L.)

Brown rice traits are critical to both grain yield and quality. In the present study, the chromosome segment substitution lines (CSSLs) population derived from a cross between japonica Koshihikari and indica Nona Bokra was used to analyze the brown rice length (BRL), brown rice width (BRW), length–width ratio of brown rice (BLWR), brown rice thickness (BRT), brown rice perimeter (BRP), brown rice area (BRA), thousand-grain weight of brown rice (BRGW), brown rice ratio (BRR), taste value of brown rice (BTV), and water content of brown rice (BWC). Correlations analysis showed that most of the brown rice traits had significant correlations with each other, except for BRR, BTV, and BWC. A total of sixty-one QTLs for these traits were identified under three environments, which mapped to chromosomes 1, 2, 3, 5, 6, 7, 8, 10, 11, and 12, with the LOD ranging from 2.52 to 16.68 and accounting for 2.60 to 25.38% of the total phenotypic variations. Moreover, thirty pairs of epistatic interactions for BRL, BRW, BLWR, BRP, and BRA were estimated and distributed on all chromosomes except 10. These findings will provide a further understanding of the genetic basis of brown rice traits and facilitate the genetic improvement of rice yield and quality through breeding.