Search Results (29)

Doubled haploid (DH) technology accelerates maize breeding by generating completely homozygous lines within two generations, but its efficiency depends on reliable haploid identification markers. The Purple plant 1 (Pl-1) root pigmentation marker has emerged as a promising alternative to R1-Navajo (R1-nj), which suffers from frequent suppression in tropical germplasm. This study evaluated Pl-1 expression and seedling vigor in 298 diverse Thai maize genotypes across four market classes under controlled growth chamber conditions (24 ± 1 °C, 85–90% humidity, and standardized lighting), followed by testcross analysis with 89 representative genotypes crossed with BHI306 to distinguish between allelic absence and epistatic suppression mechanisms. Complete absence of Pl-1 expression was observed in 99.3% of Thai genotypes, contrasting with consistent expression in the temperate-derived control (BHI306). Testcross F₁ progeny from 89 Thai × BHI306 crosses exhibited intermediate expression levels (1.57–2.05) across all market classes, confirming allelic absence rather than suppressor-mediated inhibition. Substantial genetic diversity was detected in seedling vigor traits independent of Pl-1 status, with root length varying 43-fold and fresh weight 20-fold, showing highly significant genotypic effects. The uniform lack of Pl-1 expression across Thai germplasm eliminates background interference, highlighting its utility as a complementary marker when introgressed from inducer lines. These findings establish the genetic foundation for implementing optimized DH breeding strategies in tropical maize through marker-assisted backcrossing approaches. Full article

Background/Objectives: To overcome the limitations imposed by bacterial blight on widely adopted indica–japonica hybrid rice, this study employed molecular design breeding strategies to develop a resistant germplasm. Methods: Through conventional backcross breeding combined with molecular-marker-assisted selection, the Xa23-carrying material XR39 was hybridized with the wide-compatibility restorer line R5315 harboring the S5n gene. Progeny selection integrated evaluations of agronomic traits, disease resistance identification, and test-crossing with sterile lines. Results: Five wide-compatibility restorer lines simultaneously incorporating the Xa23 and S5n genes were successfully developed, demonstrating outstanding bacterial blight resistance and restoration ability. The selected hybrid combinations, A3/RP1, A1/RP4, and A4/RP4, exhibited yield increases of 2.6–8.6% compared to the control. Conclusions: This study not only established a novel germplasm for developing bacterial blight-resistant indica–japonica hybrid rice varieties, but also established a model for gene design breeding for rice improvement. Full article

Germplasm improvement is essential for maize breeding. Currently, intra-heterotic-group crossing is the major method for germplasm improvement, while inter-heterotic-group crossing is also used in breeding but not in a systematic way. In this study, five inbred lines from four heterotic groups were used to develop a connected segregating population through inter-heterotic-group line crossing (CSPIC), which comprised 5 subpopulations with 535 doubled haploid (DH) lines and 15 related test-cross populations including 1568 hybrids. Significant genetic variation was observed in most subpopulations, with several DH populations exhibiting superior phenotypes regarding traits such as plant height (PH), ear height (EH), days to anthesis (DTA), and days to silking (DTS). Notably, 10.8% of hybrids in the population POP5/C229 surpassed the high-yielding hybrid ND678 (CK). To reduce field planting costs and quickly screen for the best inter-heterotic-group DH lines and test-cross hybrids, we assessed the accuracy of genomic selection (GS) for within- and between-population predictions in the DH populations and the test-cross populations. Within the DH or the hybrid population, the prediction accuracy varied across populations and traits, with an average hybrid yield prediction accuracy of 0.41, reaching 0.54 in POP5/Z58. In the cross DH population predictions, the prediction accuracy of the half-sib population exceeded that of the non-sib cross population prediction, with the highest accuracy observed when the non-shared parents were from the same heterotic group, and the average phenotypic prediction accuracies of POP3 predicting POP2 and POP2 predicting POP3 were 0.54 and 0.45, respectively. In the cross hybrid population predictions, the accuracy was highest when both the training and the test sets came from the same DH populations, with an average accuracy of 0.43. The proportion of shared polymorphisms with respect to SNPs between the training and the test sets (PSP) exhibited a significant and strong correlation with the prediction accuracy of cross population prediction. This study demonstrates the feasibility of creating new heterotic groups through inter-heterotic-group crossing in germplasm improvement, and some cross population prediction patterns exhibited excellent prediction accuracy. Full article

Maize (Zea mays L.) is one of the most widely cultivated grain crops globally. In sub-Saharan Africa (SSA), it plays an important role in ensuring both food and income security for smallholder farmers. This study was conducted to (i) assess the performances of testcross hybrids constituted from maize lethal necrosis (MLN) tolerant doubled haploid (DH) lines under various management conditions; (ii) estimate the combining ability effects and determine the nature of gene action in the DH lines; and (iii) identify DH lines and testcross hybrids for resistance to MLN, high grain yield, and other important traits. Eleven DH lines were crossed with 11 single-cross testers using the line-by-tester mating design, and 115 successful testcross hybrids were generated. These hybrids, along with five commercial check hybrids, were evaluated across four optimum management conditions, two MLN artificial inoculations, and one managed drought environment in Kenya. Under each management condition, the effects of genotypes, environments, and genotype-by-environment interactions were significant for grain yield (GY) and most other traits. Hybrids T1/L3, T10/L3, and T11/L3 exhibited higher grain yields under at least two management conditions. A combining ability analysis revealed that additive gene effects were more important than non-additive effects for GY and most other traits, except for leaf senescence (SEN) and MLN disease severity score. DH line L3 exhibited a desirable general combining ability (GCA) effect for GY, while L5 was the best general combiner for anthesis date (AD) and plant height (PH) across all management conditions. DH lines L2, L6, and L7 showed negative GCA effects for MLN disease severity. Single-cross testers T11 and T10 were good general combiners for GY under all management conditions. Hybrids T2/L11, T9/L10, and T2/L10 demonstrated high specific combining ability (SCA) effects for GY under all conditions. This study identified DH lines and testers with favorable GCA effects for grain yield, MLN resistance, and other agronomic traits that can be used in breeding programs to develop high-yielding and MLN-resistant maize varieties. Better-performing testcross hybrids identified in the current study could be verified through on-farm testing and released for commercial production to replace MLN-susceptible, low-yield hybrids grown in the target ecologies. Full article

Deciphering the molecular basis of heterosis would yield genes and markers for designing improved maize-hybrid varieties. In this study, 481 BC₁F₃ lines derived from Zheng58 and PH4CV were genotyped with 15,386 polymorphic SNPs markers and testcrossed with two testers (Chang7-2 and PH6WC) to generate 962 testcross lines. The yield of these testcross lines and their parental lines was evaluated across multiple environments. Genetic analysis revealed that dominance is the primary contributor to heterosis. Mapping of midparent heterosis (MPH) identified two dominant QTL, six additive-by-additive interactions, eighteen additive-by-dominance interactions, and fifty-four dominance-by-dominance interactions. These interactions encompassed 104 genetic blocks, including 24 genetic blocks that explained >1% of phenotypic variances for both MPH and hybrid performance. We compared the locations of the allele-specific expression genes (ASEGs) identified from the expression data of two hybrid lines and their parental lines with those of the 24 genetic blocks and found 15 ASEGs related to yield or biomass regulation, including two known genes BT2 and ZmNF-YC4. Fisher’s exact test analysis indicated a significant enrichment of these ASEGs in the 24 blocks, affirming the reliability of the MPH-mapping results. The co-expression network of six ASEGs, including BT2 and ZmNF-YC4, contained many genes related to yield or biomass regulation. This study unravels potential candidate genes and regulatory networks associated with maize heterosis. Full article

The improvement of grain yield, quality, and resistance can be achieved through the utilization of heterosis. The combination of cytoplasmic male sterility (CMS) and fertility restoration (Rf) gene(s) greatly facilitates the commercial development of three-line hybrid rice based on heterosis. The basis for investigating the relationship between CMS and Rf genes lies in the rapid localization of wild rice fertility restoration genes. A set of the BC₄F₅ population derived from interspecific crosses between Xieqingzao B (XB) and the BC₁F₉ XB//Dongxiang wild rice (DWR)/XB line L5339 was used to detect quantitative trait loci (QTL) for fertility restoration. The population was then crossed with two male sterile lines, Zhong9A (Z9A) and DongB11A (DB11A), in order to generate a testcrossing population for investigating spikelet fertility. Based on the linkage mapping, seven QTLs were detected on chromosomes 1, 3, 5, 6, 8, and 10, explaining 2.76 to 12.46% of the phenotypic variation. Of them, two novel fertility restoration QTLs, qRf3 and qRf6, can restore fertility of the CMS-DWR line DB11A by 16.56% and 15.12%, respectively. By employing joint QTL-seq and GradedPool-Seq methods, two novel Rf QTLs for DB11A, qRf3 and qRf6, were identified at the physical locations of 10,900,001–11,700,000 bp and 28,016,785–31,247,556 bp, respectively. These findings are useful for exploring the natural variations of Rf genes in rice. Therefore, rice’s new genetic resources for the selection and breeding of rice restorer lines provide promising candidates for QTL fine localization and clarification. Full article

Grifola frondosa is a valuable edible fungus with high nutritional and medicinal values. The mating systems of fungi not only offer practical strategies for breeding, but also have far-reaching effects on genetic variability. Grifola frondosa has been considered as a sexual species with a tetrapolar mating system based on little experimental data. In the present study, one group of test crosses and six groups of three-round mating experiments from two parental strains were conducted to determine the mating system in G. frondosa. A chi-squared test of the results of the test-cross mating experiments indicated that they satisfied Mendelian segregation, while a series of three-round mating experiments showed that Mendelian segregation was not satisfied, implying a segregation distortion phenomenon in G. frondosa. A genomic map of the G. frondosa strain, y59, grown from an LMCZ basidiospore, with 40.54 Mb and 12 chromosomes, was generated using genome, transcriptome and Hi-C sequencing technology. Based on the genomic annotation of G. frondosa, the mating-type loci A and B were located on chromosomes 1 and 11, respectively. The mating-type locus A coded for the β-fg protein, HD1, HD2 and MIP, in that order. The mating-type locus B consisted of six pheromone receptors (PRs) and five pheromone precursors (PPs) in a crossed order. Moreover, both HD and PR loci may have only one sublocus that determines the mating type in G. frondosa. The nonsynonymous SNP and indel mutations between the A₁B₁ and A₂B₂ mating-type strains and the reference genome of y59 only occurred on genes HD2 and PR1/2, preliminarily confirming that the mating type of the y59 strain was A₁B₂ and not A₁B₁. Based on the genetic evidence and the more reliable molecular evidence, the results reveal that the mating system of G. frondosa is tetrapolar. This study has important implications for the genetics and hybrid breeding of G. frondosa. Full article

Color is a crucial feature to consider when breeding and improving strains of Auricularia cornea. To uncover the mechanism of white strain formation in A. cornea, this study selected parental strains that were homozygous for the color trait and analyzed the genetic laws of A. cornea color through genetic population construction, such as test-cross, back-cross, and self-cross populations, and the statistical analysis of color trait segregation. Moreover, the study developed SSR molecular markers to construct a genetic linkage map, perform the fine mapping the color-controlling genetic locus, and verify candidate genes using yeast two-hybrid, transcriptome analysis, and different light treatments. The results of the study indicated that the color trait of A. cornea is controlled by two pairs of alleles. When both pairs of loci are dominant, the fruiting body is purple, while when both pairs of loci are recessive or one pair of loci is recessive, the fruiting body is white. Based on the linkage map, the study finely mapped the color locus within Contig9_29,619bp-53,463bp in the A. cornea genome and successfully predicted the color-controlling locus gene A18078 (AcveA), which belongs to the Velvet factor family protein and has a conserved structure domain of the VeA protein. It can form a dimer with the VelB protein to inhibit pigment synthesis in filamentous fungi. Lastly, the study validated the interaction between AcVeA and VelB (AcVelB) in A. cornea at the gene, protein, and phenotype levels, revealing the mechanism of inhibition of pigment synthesis in A. cornea. Under dark conditions, dimerization occurs, allowing it to enter the nucleus and inhibit pigment synthesis, leading to a lighter fruiting body color. However, under light conditions, the dimer content is low and cannot enter the nucleus to inhibit pigment synthesis. In summary, this study clarified the mechanism of white strain formation in A. cornea, which could aid in improving white strains of A. cornea and studying the genetic basis of color in other fungi. Full article

Apple breeding is a laborious and long-lasting process that requires qualified resources, land, time, and funds. In this study, more than 5000 F₁ apple hybrids from direct and testcrosses were analyzed. The results revealed how the phenotypic expression of the main quantitative traits of interest assessed in five half-sib families was controlled by the additive genetic effects and by non-additive effects of dominance and epistasis. The statistical number of hybrids required to ensure efficient selection increased exponentially with the number of desirable traits. The minimum number of progenies required to obtain a hybrid with associated quantitative traits of agronomic interest was highly variable. For two independent traits essential in selection (fruit size and quality), but incorporated together in the same hybrid, the statistical number was between about 30 and 300. If three more cumulative traits were added (a large number of fruits per tree, resistance/tolerance to apple scab, and powdery mildew attack), the limits increased to between 1500 and 18,000. The study highlighted the need for new apple varieties due to the narrowing of the genetic diversity of the cultivated species and how the choice of parents used in hybridizations (as well as the objectives pursued in the selection) can increase the efficiency of apple breeding. Full article

Popcorn cultivation has been growing in and has positively affected the Brazilian economy. However, these crops are grown with genotypes susceptible to diseases, generating high losses. Thus, studies aimed at obtaining resistant genotypes are particularly interesting, as popcorn is susceptible to several pathogens. The most efficient, environmentally correct, and economical method of disease control is using resistant cultivars. The present study aimed to evaluate the performance of inbred lines of popcorn and their respective testcross hybrids in terms of diseases caused by fungi. For this purpose, 15 S₇ inbred lines were crossed with five testers, four with a narrow genetic basis (inbred lines L270, L651, P1, and L70) and one with a broad genetic basis (open pollination variety PARA 172). The arrangement of treatments in incomplete blocks (lattice 10 × 10) with three replications was used. The testcross was efficient in the discrimination per se of the progenies and the testers. The inbred lines L685, L691, L696, and L684 and the PARA 172 tester showed potential resistance to P. polysora, B. maydis, and E. turcicum. The GT biplot method proved reliable in identifying efficient, responsive, and resistant inbred lines and revealing the hybrid 56 as the ideal genotype. Full article

Stem rust (SR) and leaf rust (LR) are currently the two most important rust diseases of cultivated rye in Central Europe and resistant cultivars promise to prevent yield losses caused by those pathogens. To secure long-lasting resistance, ideally pyramided monogenic resistances and race-nonspecific resistances are applied. To find respective genes, we screened six breeding populations and one testcross population for resistance to artificially inoculated SR and naturally occurring LR in multi-environmental field trials. Five populations were genotyped with a 10K SNP marker chip and one with DArTseq^TM. In total, ten SR-QTLs were found that caused a reduction of 5–17 percentage points in stem coverage with urediniospores. Four QTLs thereof were mapped to positions of already known SR QTLs. An additional gene at the distal end of chromosome 2R, Pgs3.1, that caused a reduction of 40 percentage points SR infection, was validated. One SR-QTL on chromosome 3R, QTL-SR4, was found in three populations linked with the same marker. Further QTLs at similar positions, but from different populations, were also found on chromosomes 1R, 4R, and 6R. For SR, additionally seedling tests were used to separate between adult-plant and all-stage resistances and a statistical method accounting for the ordinal-scaled seedling test data was used to map seedling resistances. However, only Pgs3.1 could be detected based on seedling test data, even though genetic variance was observed in another population, too. For LR, in three of the populations, two new large-effect loci (Pr7 and Pr8) on chromosomes 1R and 2R were mapped that caused 34 and 21 percentage points reduction in leaf area covered with urediniospores and one new QTL on chromosome 1R causing 9 percentage points reduction. Full article

Understanding the impact of gene action and combining ability on targeted traits in a hybrid breeding program is imperative. The objective of this study was to estimate the genetic effect and combining ability of S₂ super sweet corn lines on carotenoid content. Twenty S₂ lines were crossed with two hybrid testers by using the line × tester mating design. Regarding parents, forty hybrids and two commercial checks were evaluated for carotenoid content across two different growing seasons between 2019 and 2020. The result indicated that the non-additive gene action governed the inheritance of carotenoid content. Several promising S₂ lines for individual carotenoids were identified; only L₂₀ possessed different and positive GCA values for all observed carotenoids. Moreover, genotype T₂ was a promising tester to identify superior lines for creating biofortified sweet corn hybrids. Testcross hybrids with satisfactory performance, desirable SCA estimates, and involving at least one of the pairwise parents with positive and high GCA were successfully defined. Hybrid T₂ × L₂₀ had high lutein, zeaxanthin, β-cryptoxanthin, and total carotenoids contents (ranging from 12.58 to 74.01 µg/g of dry weight), whereas hybrid T₂ × L₉ showed the highest content of β-carotene (4.19 µg/g of dry weight). We propose that high GCA and line at least one of the pairwise parents be included in indirect selections for the hybrid breeding of high-carotenoid sweet corn. Full article

Effective panicle numbers (PNs) and Tiller numbers (TNs) are important traits affecting rice (Oryza sativa L.) architecture and grain yield. However, the molecular mechanisms underlying PN and TN heterosis remain unknown in rice. In addition, new PN- or TN-related genes need to be detected and discovered. In this study, in order to detect rice quantitative trait loci (QTLs) and the heterosis-related loci of PN or TN in rice, we developed a high generation recombinant inbred line (RIL) population from a cross of two elite cultivars, Luohui9 (Xian/Indica) and RPY geng (Geng/Japonica), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines, YTA (Xian/Indica) and Z7A (Geng/Japonica). Finally, nine QTLs of PN across four seasons were identified, and two QTLs of TN in 191HB were mapped. Besides this, six heterosis-related QTLs of PN and five heterosis-related QTLs of TN were located. We found that heterosis-related QTLs of PN or TN covered multiple known genes, such as MOC1, TAC1 and OsETR2. Furthermore, homologous gene analysis identified one candidate gene of PN (LOC_10g25720). Together, these findings uncover multiple heterosis-related loci, and provide a new insight into the heterosis mechanism of PN and TN in rice. Full article

Early maturity is a highly important factor in the interrelations between yield, grain moisture, and plant density, contributing to cost-efficient maize production. Landraces conserved in gene banks present a promising basis for enriching the diversity of early maize breeding material. To start and speed up the mobilization of the maize genetic resources maintained in the ex situ Maize Research Institute Zemun Polje gene bank collection, which are currently scattered, little studied, and underused, 63 landraces were selected as new potential sources of early maturity; their test-cross performance with two divergent early testers was evaluated. The majority of the landraces with a prevailed flint type (29) exhibited heterosis for yield when crossed with the Iowa Stiff Stalk Synthetic—Iowa Dent tester (102NS), out of which 20 top crosses expressed grain moisture below the defined threshold value (21.1%). The best performing landraces can be used as a starting point for a new pre-breeding programme for the broadening of flint maize breeding material. In parallel, nine landraces expressed simultaneous heterosis when crossed with the flint tester (14NS), exhibiting grain moisture above the threshold value. A simultaneous heterotic effect with two divergent inbred testers implies the existence of an independent heterotic pool. These findings will contribute to the broadening of maize breeding material for early maturity and low grain moisture at harvest, which are important goals in maize breeding. Full article

Dissecting the genetic basis of yield traits in hybrid populations and identifying the candidate genes are important for molecular crop breeding. In this study, a BC1F3:4 population, the line per se (LPS) population, was constructed by using elite inbred lines Zheng58 and PH4CV as the parental lines. The population was genotyped with 55,000 SNPs and testcrossed to Chang7-2 and PH6WC (two testers) to construct two testcross (TC) populations. The three populations were evaluated for hundred kernel weight (HKW) and yield per plant (YPP) in multiple environments. Marker–trait association analysis (MTA) identified 24 to 151 significant SNPs in the three populations. Comparison of the significant SNPs identified common and specific quantitative trait locus/loci (QTL) in the LPS and TC populations. Genetic feature analysis of these significant SNPs proved that these SNPs were associated with the tested traits and could be used to predict trait performance of both LPS and TC populations. RNA-seq analysis was performed using maize hybrid varieties and their parental lines, and differentially expressed genes (DEGs) between hybrid varieties and parental lines were identified. Comparison of the chromosome positions of DEGs with those of significant SNPs detected in the TC population identified potential candidate genes that might be related to hybrid performance. Combining RNA-seq analysis and MTA results identified candidate genes for hybrid performance, providing information that could be useful for maize hybrid breeding. Full article