F2 Population Research Articles

Identification of Transgressive Segregation for Yield and Resistance to Yellow Stem Borer (Scirpophaga incertulas Walker) in F2 Segregating Generation of Six Rice Crosses (Oryza sativa L.)

The research investigation on the occurrence of transgressive segregation in F2 populations derived from six rice crosses namely: ADT 43 X TKM 6, ADT 43 X ASD 12, ADT 45 X TKM 6, ADT 45 X ASD 12, ASD 16 X TKM 6 and ASD 16 X ASD 12 with the aim of identifying superior genotypes for yield and resistance to the yellow stem borer (Scirpophaga incertulas). This research was conducted through series of field observations for transgressive segregants at Plant Breeding Farm, Department of Genetics and Plant Breeding, Faculty of Agriculture, Annamalai University during Kharif season of 2022. The crosses involved high-yielding but susceptible female parents (ADT 43, ADT 45, ASD 16) and YSB resistant but low yielding male parents (TKM 6, ASD 12). In the F2 generation, a wide range of phenotypes was observed for yield-related traits and YSB resistance. Twelve superior transgressive segregants were identified in each cross, exhibiting increased grain yield per plant, number of productive tillers, and number of grains per panicle, coupled with high levels of resistance to YSB. The results suggest that the parents carried different alleles and genes governing yield and its component traits, allowing the accumulation of favorable alleles in the F2 progeny through recombination. The identification of these high-performing transgressive segregants provides opportunities for further evaluation and potential use in rice breeding programs to develop improved cultivars with enhanced yield and biotic stress resistance.

Identification and map-based cloning of an EMS-induced mutation in wheat gene TaSP1 related to spike architecture.

A candidate gene TaSP1 related to spike shape was cloned, and the gene-specific marker was developed to efficiently track the superior haplotype in common wheat. Spike shape, an important factor that affects wheat grain yield, is mainly defined by spike length (SPL), spikelet number (SPN), and compactness. Zhoumai32 mutant 1160 (ZM1160), a mutant obtained from ethyl methane sulfonate (EMS) treatment of hexaploid wheat variety Zhoumai32, was used to identify and clone the candidate gene that conditioned the spike shape. Genetic analysis of an F2 population derived from a cross of ZM1160 and Bainong207 suggested that the compact spike shape in ZM1160 was controlled by a single recessive gene, and therefore, the mutated gene was designated as Tasp1. With polymorphic markers identified through bulked segregant analysis (BSA), the gene was mapped to a 2.65-cM interval flanked by markers YZU0852 and MIS46239 on chromosome 7D, corresponding to a 0.42-Mb physical interval of Chinese spring (CS) reference sequences (RefSeq v1.0). To fine map TaSP1, 15 and seven recombinants were, respectively, screened from 1599 and 1903 F3 plants derived from the heterozygous F2 plants. Finally, TaSP1 was delimited to a 21.9Kb (4,870,562 to 4,892,493bp) Xmis48123-Xmis48104 interval. Only one high-confidence gene TraesCS7D02G010200 was annotated in this region, which encodes an unknown protein with a putative vWA domain. Quantitative reverse transcription PCR (qRT-PCR) analysis showed that TraesCS7D02G010200 was mainly expressed in the spike. Haplotype analysis of 655 wheat cultivars using the candidate gene-specific marker Xg010200p2 identified a superior haplotype TaSP1b with longer spike and more spikelet number. TaSP1 is beneficial to the improvement in wheat spike shape.

Phenotypic Selection to Avoid Discarding Target Genotypes for Four Fruit Traits Based on Environmental Variances in a Pineapple Cross-seedling Population

Early ripening [earlier than 1 Aug during fruit harvest time (FHT)], large fruit weight (FW; >1000 g), high sugar content [>17% soluble solids content (SSC)], and low acidity in fruit juice (<0.7%) are important breeding targets of pineapple for table fresh fruit use in Japan. We investigated the efficiency of primary selection based on the four fruit traits using 129 first-fruiting F1 offspring population of ‘Yugafu’ × ‘Yonekura’ without replicates. Separately, environmental variances were estimated by an analysis of variance using evaluation data from 50 or 49 offspring in three replicates and two-year repeats. The phenotypic distribution in the 129 F1 population approached a normal distribution (P > 0.05). The genotypic distribution was obtained as a normal distribution with the population mean as the mean and genotypic variance obtained by subtracting the environmental variance from the phenotypic variance. The target genotypes were estimated at 14.4%, 58.7%, 5.0%, and 50.0% of the F1 population for FHT, FW, SSC, and acidity, respectively. Critical phenotypic values were established as the upper (FHT and acidity) and lower (FW and SSC) limits of the critical genotypic values at the 95% probability level. The phenotypic selection was made based on the critical phenotypic value, resulting in 45.0%, 88.4%, 27.1%, and 79.1% of the offspring selected for FHT, FW, SSC, and acidity, respectively, and 12.4% simultaneously for all four fruit traits. The results showed that the phenotypic primary selection reduced the population size to 12.4%, avoiding the discarding of target genotypes with a low risk. If breeders intend to further reduce the population size, then increasing the number of traits subject to primary selection would be effective.

Genetic control of root morphology in response to nitrogen across rapeseed diversity.

Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.

A Cluster of Peronospora parasitica 13-like (NBS-LRR) Genes Is Associated with Powdery Mildew (Erysiphe polygoni) Resistance in Mungbean (Vigna radiata).

Powdery mildew (PM) caused by Erysiphe polygoni is an important foliar disease in mungbean (Vigna radiata). A previous study showed that QTL qPMRUM5-2 is a major locus for PM resistance in mungbean accession RUM5 (highly resistant). Bioinformatics analysis revealed that flanking markers of the qPMRUM5-2 covered a region of 1.93 Mb. In this study, we conducted fine mapping for the qPMRUM5-2 using the F2 population of 1156 plants of the cross between Chai Nat 60 (CN60; highly susceptible) and RUM5. PM resistance evaluation was performed under field conditions using F2:3 lines grown in three different environments. QTL analyses consistently located the qPMRUM5-2 to a 0.09 cm interval on linkage group 6 between InDel markers VrLG6-InDel05 and VrLG6-InDel10, which corresponded to a 135.0 kb region on chromosome 8 containing nine predicted genes of which five were NBS-LRR-type genes Recognition of Peronospora parasitica 13-like protein (RPP13L). Whole-genome re-sequencing of RUM5 and CN60 showed polymorphisms in four RPP13L genes predictively cause substantial amino acid changes, rendering them important candidate genes for PM resistance. The InDel markers VrLG6-InDel05 and VrLG6-InDel10 flanking to the qPMRUM5-2 would be useful for marker-assisted breeding of PM resistance in the mungbean.

Studies on Screening and Inheritance of Yellow Stem Borer (Scirpophaga incertulas Walker) Resistance in F2 and F3 Segregating Generations of Rice (Oryza sativa L.)

This study investigated the screening and inheritance of resistance to yellow stem borer (Scirpophaga incertulas) in F2 and F3 segregating generations of rice (Oryza sativa L.) derived from six crosses viz., ADT 43 X TKM 6, ADT 43 X ASD 12, ADT 45 X TKM 6, ADT 45 X ASD 12, ASD 16 X TKM 6 and ASD 16 X ASD 12. Field screening was conducted during the 2021 and 2022 kharif seasons, evaluating white ear damage as an indicator of resistance. The F2 and F3 populations showed a range of resistance levels from highly resistant to highly susceptible across the six crosses of rice. The distribution of resistance varied, with the cross ASD 16 x TKM 6 having the highest number of highly resistant plants in F2, while ADT 45 x ASD 12 had the lowest in both generations. Chi-square analysis revealed that the inheritance of resistance followed a complementary gene action epistasis with a 9-resistant to 7 susceptible ratios observed in all six crosses across both generations. The screening helped identify promising yellow stem borer resistant segregants, which can be further investigated at the genomic level for molecular characterization and mapping of resistance QTLs to facilitate their introgression into rice breeding programs.

An aldehyde dehydrogenase gene, GhALDH7B4_A06, positively regulates fiber strength in upland cotton (Gossypium hirsutum L.).

High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length-amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74-90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S. Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular breeding.

Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa).

In an ethyl methanesulfonate oat (Avena sativa) mutant population we have found a mutant with striking differences to the wild-type (WT) cv. Belinda. We phenotyped the mutant and compared it to the WT. The mutant was crossed to the WT and mapping-by-sequencing was performed on a pool of F2 individuals sharing the mutant phenotype, and variants were called. The impacts of the variants on genes present in the reference genome annotation were estimated. The mutant allele frequency distribution was combined with expression data to identify which among the affected genes was likely to cause the observed phenotype. A brassinosteroid sensitivity assay was performed to validate one of the identified candidates. A literature search was performed to identify homologs of genes known to be involved in seed shape from other species. The mutant had short kernels, compact spikelets, altered plant architecture, and was found to be insensitive to brassinosteroids when compared to the WT. The segregation of WT and mutant phenotypes in the F2 population was indicative of a recessive mutation of a single locus. The causal mutation was found to be one of 123 single-nucleotide polymorphisms (SNPs) spanning the entire chromosome 3A, with further filtering narrowing this down to six candidate genes. In-depth analysis of these candidate genes and the brassinosteroid sensitivity assay suggest that a Pro303Leu substitution in AVESA.00010b.r2.3AG0419820.1 could be the causal mutation of the short kernel mutant phenotype. We identified 298 oat proteins belonging to orthogroups of previously published seed shape genes, with AVESA.00010b.r2.3AG0419820.1 being the only of these affected by a SNP in the mutant. The AVESA.00010b.r2.3AG0419820.1 candidate is functionally annotated as a GSK3/SHAGGY-like kinase with homologs in Arabidopsis, wheat, barley, rice, and maize, with several of these proteins having known mutants giving rise to brassinosteroid insensitivity and shorter seeds. The substitution in AVESA.00010b.r2.3AG0419820.1 affects a residue with a known gain-of function substitution in Arabidopsis BRASSINOSTEROID-INSENSITIVE2. We propose a gain-of-function mutation in AVESA.00010b.r2.3AG0419820.1 as the most likely cause of the observed phenotype, and name the gene AsGSK2.1. The findings presented here provide potential targets for oat breeders, and a step on the way towards understanding brassinosteroid signaling, seed shape and nutrition in oats.

Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq)

Coix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi. This map was constructed using an F2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi. They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi.

Inbreeding Depression and Genetic Diversity of S1 Lines Corn Plants Under Drought Stress Conditionson Dry Land

Selfing was carried out on the F2 population of corn plants and the S1 line was produced. Selfing is carried out to form pure lines in order to create hybrids. The aim of the research was to determine the magnitude of inbreeding depression, genetic diversity and heritability of leaf angle trait, yield and harvest age of the S1 line of corn plants under drought stress conditions in dry land. The experiment was carried out from March to June 2023 in Gumantar village, North Lombok district. The design used was a randomized block design, two replications. The number of treatments was 31, namely 30 S1 lines and an F2 population. Plantings are given heavy stress. Observed variables include flowering, growth, harvest age, yield components and yield. The level of inbreeding depression is based on the F2 population and is expressed as a percent. Genetic diversity is calculated based on the results of analysis of variance at a significance level of 5 percent. The results showed that inbreeding depression in leaf angle and harvest age of the S1 lines were relatively low; while the yield is classified as high. Broad categories of genetic diversity were obtained in the yield; while the leaf angle and harvest age are relatively narrow. Broad sense heritability was relatively high in the yield; while the leaf angle is classified as medium and the harvest age is relatively low. The selection of S1 lines should be based on yield, namely lines that have the same yield as the F2 population.

Broad-Spectrum Resistance and Monogenic Inheritance of Bacterial Blight Resistance in an Indigenous Upland Rice Germplasm ULR207

Bacterial blight (BB) caused by Xanthomonas oryzae pv. Oryzae (Xoo) is a serious disease of rice worldwide that can reduce crop yield and affect food insecurity. A rice resistance variety is an alternate way to solve this problem. The broad-spectrum resistance (BSR) of ULR207 is important for durable resistance to several of the Xoo isolates. However, the inheritance of this resistance gene in ULR207 must be known before it can be utilized. Thus, this study aimed to survey the BB resistance gene with reference to the BB resistance gene for identification of non-analogous or analogous genes and confirmation of a broad-spectrum resistance, to investigate the gene effect, the number of genes, and the heritability of the BB resistance gene in the ULR207 variety. Six populations of two crosses (Maled Phai × ULR207 and RD6 × ULR207), i.e., ULR207 (Donor parent), Maled Phai and RD6 (Recurrent parent), F1, F2, BC1P1, and BC1P2 were constructed. These materials were evaluated for BB resistance by clipping methods under greenhouse conditions using a virulence isolate of a pathogen in Thailand. The results showed that ULR207 exhibited the strongest against BB with 0.8 of BSR with low area under the disease progress curve (AUDPC). Molecular screening for surveying of the BB resistance gene in ULR207 revealed a non-analogous resistance gene with resistance check varieties. The phenotype of the disease lesion length of F2 and BC1P2 populations exhibited a ratio of 1:3 and 1:1 (resistant: susceptible), respectively, revealing a single recessive gene in both crosses. The scaling test parameters A, B, and C were non-significant (p < 0.01), indicating that variation in data was sufficiently explained by additive (d) and dominance (h) components. The gene action of ULR207 was controlled by additive gene action. Heritability of the two crosses, Maled Phai x ULR207 and RD6 x ULR207, exhibited high values with 0.817 and 0.716, whereas the numbers of the genes were 1.4 and 1.2, respectively. The result indicated that the breeding strategy could be employed in early generations when using ULR207 as a new source of bacterial blight resistance.

Fine mapping and targeted genomic analyses of photoperiod‐sensitive gene (GB_PPD1) in Pima cotton (Gossypium barbadense L.)

AbstractCotton grown in the United States are day‐length insensitive annuals and are grown under long‐day summers. Photoperiod sensitivity, present in tropical wild and landraces endemic to the center of origin and diversity, is a major barrier for the introgression of tropical gene pool into the US cotton. Previously, we mapped the major photoperiod response locus Gb_Ppd1 on chromosome D06 of Pima cotton (Gossypium barbadense L.). In the current study, an F2 population of 2112 gametes was used to fine map the Gb_Ppd1 locus. Two sequence‐tagged‐site and nine kompetitive allele‐specific polymerase chain reaction (KASP) markers were developed and the Gb_Ppd1 locus was fine mapped to 1.1 cM region flanked by novel markers 17‐KASP‐8, 17‐KASP‐10, and 15‐PR‐10A. The closely linked markers identified 2.10 Mb region in the G. barbadense genome that contained 18 putative gene sequences. A candidate gene Gbar_D06G014560 showed high homology to VASCULAR PLANT ONE ZINC FINGER PROTEIN 1 involved in photoperiodism in Arabidopsis. We evaluated the diagnostic polymorphisms for the flanking markers on a diversity panel of 91 Pima accessions. These markers would be useful in marker‐assisted selection of photoperiod response in cotton breeding. Further, quantitative gene expression analysis indicated that the CONSTANS (CO)/FLOWERING LOCUS T (FT) system is conserved in the photoperiod response pathway in Pima cotton, while CO and FT are likely not the causal genes underlying flowering time at the Gb_Ppd1 locus. The Gb_Ppd1 gene may be an upstream regulatory sequence in the FT gene pathway that controls photoperiodism in photoperiod‐sensitive cotton by affecting the CO/FT interaction under long‐day‐length conditions.

Globally deployed sorghum aphid resistance gene RMES1 is vulnerable to biotype shifts but is bolstered by RMES2.

Durable host plant resistance (HPR) to insect pests is critical for sustainable agriculture. Natural variation exists for aphid HPR in sorghum (Sorghum bicolor), but the genetic architecture and phenotype have not been clarified and characterized for most sources. In order to assess the current threat of a sorghum aphid (Melanaphis sorghi) biotype shift, we characterized the phenotype of Resistance to Melanaphis sorghi 1 (RMES1) and additional HPR architecture in globally admixed populations selected under severe sorghum aphid infestation in Haiti. We found RMES1 reduces sorghum aphid fecundity but not bird cherry-oat aphid (Rhopalosiphum padi) fecundity, suggesting a discriminant HPR response typical of gene-for-gene interaction. A second resistant gene, Resistance to Melanaphis sorghi 2 (RMES2), was more frequent than RMES1 resistant alleles in landraces and historic breeding lines. RMES2 contributes early and mid-season aphid resistance in a segregating F2 population; however, RMES1 was only significant with mid-season fitness. In a fixed population with high sorghum aphid resistance, RMES1 and RMES2 were selected for demonstrating a lack of severe antagonistic pleiotropy. Associations with resistance colocated with cyanogenic glucoside biosynthesis genes support additional HPR sources. Globally, therefore, an HPR source vulnerable to biotype shift via selection pressure (RMES1) is bolstered by a second common source of resistance in breeding programs (RMES2), which may be staving off a biotype shift and is critical for sustainable sorghum production.

An R2R3-MYB Transcriptional Factor LuMYB314 Associated with the Loss of Petal Pigmentation in Flax (Linum usitatissimum L.).

The loss of anthocyanin pigments is one of the most common evolutionary transitions in petal color, yet the genetic basis for these changes in flax remains largely unknown. In this study, we used crossing studies, a bulk segregant analysis, genome-wide association studies, a phylogenetic analysis, and transgenic testing to identify genes responsible for the transition from blue to white petals in flax. This study found no correspondence between the petal color and seed color, refuting the conclusion that a locus controlling the seed coat color is associated with the petal color, as reported in previous studies. The locus controlling the petal color was mapped using a BSA-seq analysis based on the F2 population. However, no significantly associated genomic regions were detected. Our genome-wide association study identified a highly significant QTL (BP4.1) on chromosome 4 associated with flax petal color in the natural population. The combination of a local Manhattan plot and an LD heat map identified LuMYB314, an R2R3-MYB transcription factor, as a potential gene responsible for the natural variations in petal color in flax. The overexpression of LuMYB314 in both Arabidopsis thaliana and Nicotiana tabacum resulted in anthocyanin deposition, indicating that LuMYB314 is a credible candidate gene for controlling the petal color in flax. Additionally, our study highlights the limitations of the BSA-seq method in low-linkage genomic regions, while also demonstrating the powerful detection capabilities of GWAS based on high-density genomic variation mapping. This study enhances our genetic insight into petal color variations and has potential breeding value for engineering LuMYB314 to develop colored petals, bast fibers, and seeds for multifunctional use in flax.

Identification of Chromosomal Regions and Candidate Genes for Round leaf Locus in Cucumis melo L.

Leaf morphology plays a crucial role in plant classification and provides a significant model for studying plant diversity while directly impacting photosynthetic efficiency. In the case of melons, leaf shape not only influences production and classification but also represents a key genetic trait that requires further exploration. In this study, we utilized forward genetics to pinpoint a recessive locus, dubbed Cmrl (Round leaf), which is responsible for regulating melon leaf shape. Through bulked segregant analysis sequencing and extensive evaluation of a two-year F2 population, we successfully mapped the Cmrl locus to a 537.07 kb region on chromosome 8 of the melon genome. Subsequent genetic fine-mapping efforts, leveraging a larger F2 population encompassing 1322 plants and incorporating F2:3 phenotypic data, further refined the locus to an 80.27 kb interval housing five candidate genes. Promoter analysis and coding sequence cloning confirmed that one of these candidates, MELO3C019152.2 (Cmppr encoding a pentatricopeptide repeat-containing family protein, Cmppr), stands out as a strong candidate gene for the Cmrl locus. Notably, comparisons of Cmrl expressions across various stages of leaf development and different leaf regions suggest a pivotal role of Cmrl in the morphogenesis of melon leaves.

Trait‐dependent plasticity erodes rapidly with repeated intergenerational acclimation in an invasive agricultural pest

AbstractClimate change is associated with increased mean temperatures and amplitudes manifesting both acutely and chronically, triggering organism stress responses that confer fitness costs and/or benefits. The larger grain borer (LGB), Prostephanus truncatus (Horn) (Coleoptera: Bostrichidae) is an invasive postharvest agricultural pest. While host shift is its well‐known potential invasive mechanism, how repeated intergenerational stress environments may influence offspring phenotypes is largely unknown. We thus evaluated physiological and ecological performance of LGB following repeated intergenerational acute heat acclimation to insinuate its likely responses to projected increased bouts of heat stress associated with climate change. Parental colonies were acutely heat‐acclimated separately at 35°C and 38°C; 80% RH for 2 h in climate chambers and released onto sterilized maize grain at optimal conditions (32°C, 80% RH). The F1 progenies were, respectively, acclimated at the same conditions and incubated to F2 generation. We then evaluated physiological and ecological performance under optimal conditions across parental, F1 and F2 generations. Our results showed that plasticity was highly trait dependent, and that acclimation did not affect F1 and F2 critical thermal maxima, but did improve critical thermal minima. However, while acclimation improved heat knockdown time at F1, repeated acclimation significantly reduced heat knockdown times at F2, suggesting plasticity erosion with generational repeated acclimations. Acute acclimation negatively affected ecological performance of F1 generations although this was restored with repeated acclimation in F2 populations. Our results suggest that the LGB may inflict more economic damage with repeated heat stress due to generational adaptation to temperature stress. The results contribute to knowledge on pest forecasting modelling under changing climates and provides a framework for phytosanitary adjustments in heat treatment protocols for international grain trade.

Fine mapping of TFL, a major gene regulating fruit length in snake gourd (Trichosanthes anguina L).

Fruit length is a crucial agronomic trait of snake gourd (Trichosanthes anguina L); however, genes associated with fruit length have not been characterised. In this study, F2 snake gourd populations were generated by crossing the inbred lines, S1 and S2 (fruit lengths: 110 and 20cm, respectively). Subsequently, bulk segregant analysis, sequencing, and fine-mapping were performed on the F2 population to identify target genes. Our findings suggest that the fruit length of snake gourd is regulated by a major-effect regulatory gene. Mining of genes regulating fruit length in snake gourd to provide a basis for subsequent selection and breeding of new varieties. Genotype-phenotype association analysis was performed on the segregating F2 population comprising 6,000 plants; the results indicate that the target gene is located on Chr4 (61,846,126-61,865,087bp, 18.9-kb interval), which only carries the annotated candidate gene, Tan0010544 (designated TFL). TFL belongs to the MADS-box family, one of the largest transcription factor families. Sequence analysis revealed a non-synonymous mutation of base C to G at position 202 in the coding sequence of TFL, resulting in the substitution of amino acid Gln to Glu at position 68 in the protein sequence. Subsequently, an InDel marker was developed to aid the marker-assisted selection of TFL. The TFL in the expression parents within the same period was analysed using quantitative real-time PCR; the TFL expression was significantly higher in short fruits than long fruits. Therefore, TFL can be a candidate gene for determining the fruit length in snake gourd. Collectively, these findings improve our understanding of the genetic components associated with fruit length in snake gourds, which could aid the development of enhanced breeding strategies for plant species.

QTL mapping and candidate gene analysis reveal two major loci regulating green leaf color in non-heading Chinese cabbage.

Two major-effect QTL GlcA07.1 and GlcA09.1 for green leaf color were fine mapped into 170.25kb and 191.41kb intervals on chromosomes A07 and A09, respectively, and were validated by transcriptome analysis. Non-heading Chinese cabbage (NHCC) is a leafy vegetable with a wide range of green colors. Understanding the genetic mechanism behind broad spectrum of green may facilitate the breeding of high-quality NHCC. Here, we used F2 and F7:8 recombination inbred line (RIL) population from a cross between Wutacai (dark-green) and Erqing (lime-green) to undertake the genetic analysis and quantitative trait locus (QTL) mapping in NHCC. The genetic investigation of the F2 population revealed that the variation of green leaf color was controlled by two recessive genes. Six pigments associated with green leaf color, including total chlorophyll, chlorophyll a, chlorophyll b, total carotenoids, lutein, and carotene were quantified and applied for QTL mapping in the RIL population. A total of 7 QTL were detected across the whole genome. Among them, two major-effect QTL were mapped on chromosomes A07 (GlcA07.1) and A09 (GlcA09.1) corresponding to two QTL identified in the F2 population. The QTL GlcA07.1 and GlcA09.1 were further fine mapped into 170.25kb and 191.41kb genomic regions, respectively. By comparing gene expression level and gene annotation, BraC07g023810 and BraC07g023970 were proposed as the best candidates for GlcA07.1, while BraC09g052220 and BraC09g052270 were suggested for GlcA09.1. Two InDel molecular markers (GlcA07.1-BcGUN4 and GlcA09.1-BcSG1) associated with BraC07gA023810 and BraC09g052220 were developed and could effectively identify leaf color in natural NHCC accessions, suggesting their potential for marker-assisted leaf color selection in NHCC breeding.

Early-Generation Evaluation of Marker-Assisted Transfer of bmr6 and bmr12 Alleles into Sweet and High-biomass Sorghum

The effects of transferring brown midrib (bmr) alleles in sweet and high biomass sorghums (SS/HBM) are not fully understood, and available works produced mixed results depending upon the genetic background of the recurrent parent used. Early-generation testing of the effects of the two mutations in the background of the recurrent parents can help predict the final products and make appropriate early go/no-go breeding decisions, yet, this information is missing. The present study was therefore carried out to reduce these gaps. Marker-assisted transfer of the bmr6 and bmr12 was performed using four (SSV84, ICSB474, ICSV18003, ICSV100324) SS and one (ICSV15024) HBM wild type (WT) lines as recurrent parents, and one bmr6 (N609) and two bmr12 (ICSV101039 and N600) lines as donor parents. Crossing and backcrossing techniques were used to transfer the bmr alleles to develop BC2F2 and F3 populations. Kompetitive allele-specific PCR (KASP) marker genotyping assays were performed and implemented for the indirect selection of the bmr transfer in F1 and BC_F1 populations. While the bmr6 markers were polymorphic, the bmr12 markers were monomorphic. The successful bmr6 transfer was therefore confirmed by markers in F1 and BC_F1, while for bmr12 the transfer was confirmed after segregation assessment in F2 and BC_F2 populations. The transfer of bmr12 improved the cellulose content relative to WT genotypes, and bmr12 populations were shorter-statured relative to bmr6 individuals, meaning that bmr12 gene can be considered in sorghum breeding to boost 2G bioethanol bioconversion and to control lodging, and hence favouring mechanical harvesting and limiting yield losses. The observed earliness in the bmr lines is an attractive trait conferring adaptation in the drylands, particularly in the world’s semi-arid tropics characterized by terminal drought stress. Both bmr alleles did not show any negative trade-offs relative to the must-have sorghum plant characteristics, implying that they can safely be deployed in sorghum breeding for bioenergy production purposes. The observed superior bmr lines with farmer-preferred phenotypic acceptance are candidates not only for advancement in breeding pipelines but also for subsequent pyramiding bmr6 and bmr12 in the same genetic background, further improving the bmr-conferred benefits. The successfully used molecular markers will be uploaded in the public domain and can help breed sorghum products other than SS/HBM such as high-quality forage sorghums.

Transcriptional Regulation and Gene Mapping of Internode Elongation and Late Budding in the Chinese Cabbage Mutant lcc.

Two important traits of Chinese cabbage, internode length and budding time, destroy the maintenance of rosette leaves in the vegetative growth stage and affect flowering in the reproductive growth stage. Internodes have received much attention and research in rice due to their effect on lodging resistance, but they are rarely studied in Chinese cabbage. In Chinese cabbage, internode elongation affects not only the maintenance of rosette leaves but also bolting and yield. Budding is also an important characteristic of Chinese cabbage entering reproductive growth. Although many studies have reported on flowering and bolting, studies on bud emergence and the timing of budding are scarce. In this study, the mutant lcc induced by EMS (Ethyl Methane Sulfonate) was used to study internode elongation in the seedling stage and late budding in the budding stage. By comparing the gene expression patterns of mutant lcc and wild-type A03, 2280 differentially expressed genes were identified in the seedling stage, 714 differentially expressed genes were identified in the early budding stage, and 1052 differentially expressed genes were identified in the budding stage. Here, the transcript expression patterns of genes in the plant hormone signaling and clock rhythm pathways were investigated in relation to the regulation of internode elongation and budding in Chinese cabbage. In addition, an F2 population was constructed with the mutants lcc and R500. A high-density genetic map with 1602 marker loci was created, and QTLs for internode length and budding time were identified. Specifically, five QTLs for internode length and five QTLs for budding time were obtained. According to transcriptome data analysis, the internode length candidate gene BraA02g005840.3C (PIN8) and budding time candidate genes BraA02g003870.3C (HY5-1) and BraA02g005190.3C (CHS-1) were identified. These findings provide insight into the regulation of internode length and budding time in Chinese cabbage.