F2 Plants Research Articles

Inheritance of resistance to three endemic viral diseases of cowpea in Nigeria

ABSTRACT Mosaic diseases, caused by bean common mosaic virus-blackeye cowpea mosaic strain (BCMV-BlCM), southern bean mosaic virus (SBMV), and cucumber mosaic virus (CMV), hamper the productivity of cowpea (Vigna unguiculata (L.) Walp.). Under single or mixed infections, these endemic viruses significantly reduce cowpea yield in sub-Saharan Africa. Planting resistant varieties is the most effective control method. Knowledge of the mode of inheritance of viral resistance is crucial in developing resistant varieties. Inheritance of resistance to BCMV-BlCM, SBMV, and CMV was investigated in two improved cowpea breeding lines. For BCMV-BICM, crosses were made between resistant IT97K-1042-3 (female) and susceptible IT99K-1060 (male); for SBMV, between resistant IT98K-1092-1 (male) and susceptible IT99K-1060 (female); and for CMV, between tolerant IT98K-1092-1 (female) and susceptible IT99K-573-1-1 (male). The F1 progenies were advanced to F2, and some F1 plants were backcrossed to the two parental lines. Reciprocal crosses were made and the 7-day-old seedlings of P1, P2, F1, F2, BCP1, and BCP2 were phenotyped by mechanical inoculation with BCMV-BlCM, SBMV, and CMV under screenhouse conditions. Data on disease incidence and severity were taken at weekly intervals for 5-week post-inoculation. Virus infections were confirmed via antigen-coated plate enzyme-linked immunosorbent assay or reverse transcription-polymerase chain reaction. Chi-square analysis of the genetic segregation indicated that a recessive gene pair in IT97K-1042-3 controlled the inheritance of resistance to BCMV-BlCM. Duplicate dominant genes conditioned the resistance to SBMV and tolerance to CMV in IT98K-1092-1. The backcrosses confirmed the monogenic and digenic inheritance patterns, whereas reciprocal crosses indicated absence of cytoplasmic effects.

Trans-generational response of TiO2 nanoparticles in inducing variability and changes in biochemical pool of lentil F2 progenies

Investigations were carried out to analyze the role of anatase nanoparticles in inducing genetic variability in lentils (Lens culinaris Medik.) for yield improvement and subsequent involvement in development, quality, and biochemical response of second-generation seedlings through their lifecycle. Trans-generational alterations in the morphological and biochemical pool of the plant system were evaluated over a range of concentrations (25-200 µg/mL). Analysis of F2 seedlings showed an increase in yield parameters at the lowest concentration (25 µg/mL). Biochemical studies revealed that the F2 plants experienced lower oxidative stress as compared with previous generation plants. Quality analysis of seeds revealed a slight positive shift in the mean values of seed protein content at the lowest concentration. The effect of nanoparticles on the growth parameters was antagonistic except at the lowest concentration, where the growth parameters were found to be slightly higher than in the controls. The variability present in different traits in the F2 populations was quantified as phenotypic variability and its components, which is a measure of the transmissibility of variations of the so-called mutated populations as a result of nanoparticle application.

Effect of Meloidogyne incognita and Fusarium oxysporum f. sp. lycopersici on tomato varietal growth under Ghanaian field conditions

The excessive build-up of soil nematodes and uncontrolled spread of fungal diseases contribute to low yields in tomato (Solanum lycopersicum L.) production. The objective of this study was to investigate the pathogenicity of Fusarium oxysporum f.sp. lycopersici and Meloidogyne incognita on growth, yield and wilt severity in tomato varieties. A factorial experiment was laid out in a randomised complete block design (RCBD), with three replications, on two fields, namely University of Ghana, Legon farm and at the National Service Demonstration Farm at Papao both in Ghana, from July 2018 to June 2019. Two tomato varieties, namely Mongal F1 and Petomech were used for evaluation. Fusarium inoculum of 1.3×106 cells per 5 mL suspension was inoculated in the experimental plots naturally infested with Meloidogyne incognita, at 7, 14, and 21 days (NF7, NF14, NF21), after transplanting tomato seedlings into the fields. Wilt severity was higher in the Petomech plants compared to Mongal plants, for all treatments. Wilt incidence was greater than 70% in the Petomech plants that received the treatments NF7, NF14, and NF21 in both experimental sites, respectively. Plants in the control plots had the least wilt incidence and severity among the two varieties in both sites. Mongal and Petomech plants without Fusarium inoculation had lower wilt incidence and severity compared to those that received only Fusarium inoculation. Yield was higher in the Mongal plants than in the Petomech plants. Galls scores were zero in the Mongal F1 plants for all treatments applied, in both experimental sites. Fusarium oxysporum f. sp. lycopersici and Meloidogyne incognita increase wilt severity in tomato plants when both pathogens coexist in the soil.

Identification and validation of quantitative trait loci for a parameter associated with nitrogen partitioning to grain using a population derived from japonica- and indica-type cultivars of rice (Oryza sativa L.)

ABSTRACT Nitrogen (N) partitioning to grain affects productivity and grain quality in rice. The objectives of this study were to clarify the difference between the rice cultivars ‘Momiroman’ (japonica) and ‘Takanari’ (indica) in the relation between the amount of total N in aboveground parts per grain dry weight (TNA/GW) and grain N concentration (GNC), to identify quantitative trait loci (QTLs) associated with the coefficient characterizing this relation by using populations derived from a cross between Momiroman and Takanari, and to verify the effects of the detected QTLs by using near-isogenic lines (NILs). We used 156 F2 plants grown under high N in 2015 and 156 F3 lines grown under high or low N in 2016, and determined N concentrations and contents in grain and aboveground vegetative parts. We found a logarithmic relation between GNC and TNA/GW in Momiroman and Takanari. The regression coefficient (A) was higher in Takanari. Under each N condition, A was calculated for each population and QTL analysis was performed. QTLs for A were detected on chromosomes (Chrs.) 6 and 10 in all conditions; the Takanari alleles of both QTLs increased the value. NILs with the Takanari allele in each region had higher A than NILs with the Momiroman alleles. We conclude that the QTLs for A are associated with N partitioning to grain in rice. Abbreviations: GNA, amount of N in grain; GNC, grain N concentration; GW, grain dry weight; TNA, amount of N in aboveground parts

High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (Chenopodium quinoa Willd.).

Quinoa is a pseudocereal originating from the Andean regions. Despite quinoa’s long cultivation history, genetic analysis of this crop is still in its infancy. We aimed to localize quantitative trait loci (QTL) contributing to the phenotypic variation of agronomically important traits. We crossed the Chilean accession PI-614889 and the Peruvian accession CHEN-109, which depicted significant differences in days to flowering, days to maturity, plant height, panicle length, and thousand kernel weight (TKW), saponin content, and mildew susceptibility. We observed sizeable phenotypic variation across F2 plants and F3 families grown in the greenhouse and the field, respectively. We used Skim-seq to genotype the F2 population and constructed a high-density genetic map with 133,923 single nucleotide polymorphism (SNPs). Fifteen QTL were found for ten traits. Two significant QTL, common in F2 and F3 generations, depicted pleiotropy for days to flowering, plant height, and TKW. The pleiotropic QTL harbored several putative candidate genes involved in photoperiod response and flowering time regulation. This study presents the first high-density genetic map of quinoa that incorporates QTL for several important agronomical traits. The pleiotropic loci can facilitate marker-assisted selection in quinoa breeding programs.

Combined use of specific length amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) for rapid identification of genes influencing fiber content of hemp (Cannabis sativa L.)

Hemp (Cannabis sativa L.), an ancient crop, is a significant source of high-quality fiber that primarily caters to the textile industry worldwide. Fiber content is a crucial quantitative trait for evaluating fiber yield in hemp. Understanding the genetic mechanisms involved in hemp breeding is essential for improving yield. In this study, we developed 660 F1 plants from a cross between Jindao-15 (high fiber content fiber-use variety) and Fire No.1 (low fiber content fiber-use variety), and thirty plants each with high and low fiber content were selected from 305 monoecious plants of this population according to 5%-10% of population size for quantitative traits. The DNA from these plants was extracted to establish two bulk DNA pools and then subjected to the restriction digestion by the enzymes RsaI and HaeIII to obtain 314–364 bp digestion fragments and subjected to sequencing using specific length amplified fragment sequencing (SLAF-seq). Finally, we successfully developed 368,404 SLAF tags, which led to the detection of 25,133 high-quality SNPs. Combing with the resequencing results of parents, the SNPs of mixed pools were then subjected to the SNP-Index correlation algorithm, which revealed four candidate regions related to fiber content traits on Chromosome 1, with a length of 8.68 Mb and containing 389 annotated genes. The annotation information and the comparison results identified 15 genes that were highly likely to modulate the fiber content of hemp. Further, qPCR validation identified six genes (LOC115705530, LOC115705875, LOC115704794, LOC115705371, LOC115705688 and LOC115707511) that were highly positively correlated with influencing the hemp fiber content. These genes were involved in the transcription regulation, auxin and water transportion, one carbon and sugar metabolism. And non-synnoumous mutation SNPs which may play vital role in influencing the fiber content were detected in LOC115705875, LOC115704794, LOC115705688 and LOC115707511. Thus, our study highlights the importance of the combined use of SLAF-Seq and Bulked Segregant analysis (BSA) to locate genes related to hemp fiber content rapidly. Hence, our study provides novel mechanistic inputs for the fast identification of genes related to important agronomic traits of hemp and other crops catering to the textile industry.

Genetic Mapping and Candidate Gene Prediction of a QTL Related to Early Heading on Wild Emmer Chromosome 7BS in the Genetic Background of Common Wheat

Heading date (HD) is an essential agronomic objective in wheat conventional breeding. Field experiments from several years and locations indicated that the chromosome arm substitution line (CASL) of wild emmer chromosome 7BS in the genetic background of common wheat var. Chinese Spring (CS) always showed a substantially earlier HD than CS planted in different seasons; usually about 8 d earlier than CS grown under a normal autumn sowing season. CASL7BS consistently showed a much earlier HD than CS when treated for vernalization under a long or short photoperiod and then grown under a short or long photoperiod in the growth room. CASL7BS showed faster spike development than CS at the stages before the glume stage when grown under long days, and depicted relatively rapid growth at all stages when grown under short days. To map the early gene in CASL7BS, F2 plants from the cross of CASL7BS and CS were planted in the field and growth room, forming two mapping populations (P1 and P2, respectively). According to the HD distribution of P1, the HD was most likely regulated by a dominant gene. A QTL was detected consistently in the distal region of about 8.94 cM flanked by C268 and C309 with LOD scores of 5–8, explaining 9.14 and 12.35% of the phenotypic variation in the two mapping populations. The QTL was further narrowed down to an interval between ZAFU058724 and ZAFU061354 of 58–61 Mb based on the HD and genotype of F3 and F4 families. A total of 41 genes were located in this region, and eleven of them were thought to be the candidate genes based on the gene functions. According to the HD and mapping location, the QTL identified in this study was a new gene associated with flowering, which will be helpful in understanding the mechanism of wheat flowering and for breeding an early wheat variety.

Diversity and similarity of wheat powdery mildew resistance among three allelic functional genes at the Pm60 locus.

Cultivated wheat is continually exposed to various pathogens. Blumeria graminis f. sp. tritici (Bgt) causes powdery mildew disease and significant yield loss. Pm60 was cloned from Triticum urartu and confers race-specific powdery mildew resistance in wheat. Pm60a and Pm60b are allelic variants of Pm60 and have two leucine-rich repeat motifs deletions and insertions, respectively, which were detected in other T. urartu accessions. Through map-based cloning, virus-induced gene silencing, and stable transformation assays, we demonstrated that Pm60a and Pm60b conferred Bgt E09 resistance resembling that provided by Pm60. However, the homozygous Pm60a (but not Pm60 or Pm60b) transformants driven by the native promoters lacked race-specific resistance when they were inoculated with Bgt E18. As all three T. urartu accessions contained the three foregoing alleles, they had high resistance to Bgt E18. Pyramiding Pm60a with either of the allelic genes in F1 plants did not cause mutual allele suppression or interference with Bgt E18 resistance. Deletion (but not insertion) of the two leucine-rich repeat motifs in Pm60a substantially narrowed the resistance spectrum. In T. urartu accession PI428210, we identified another locus adjacent to Pm60a and resistant to Bgt E18. Characterization of the alleles at the Pm60 locus revealed their diversity and similarity and may facilitate wheat breeding for resistance to powdery mildew disease caused by B. graminis f. sp. tritici.

Marker-Assisted Improvement of Bread Wheat Variety HD2967 for Leaf and Stripe Rust Resistance.

The mega wheat variety HD2967 was improved for leaf and stripe rust resistance by marker-assisted backcross breeding. After its release in 2011, HD2967 became susceptible to stripe rust and moderately susceptible to leaf rust. The leaf rust resistance gene LrTrk was transferred into HD2967 from the durum wheat genotype Trinakria. Then, HD2967 was crossed with Trinakria to produce F1 plant foreground selection for LrTrk and background selection for the recurrent parent genotype was carried out in BC1F1, BC2F1 and BC2F2 generations. Foreground selection was carried out with the linked marker Xgwm234, while polymorphic SSR markers between parents were used for background selection. Background selection resulted in the rapid recovery of the recurrent parent genome. A morphological evaluation of 6 near isogenic lines (NILs)—2 resistant to leaf and stripe rust, and 4 resistant to leaf rust only—showed no significant differences in yields among NILs and the recurrent parent HD2967. All of the 6 NILs showed the presence of 2NS/2AS translocation, carrying the linked genes Lr37/Sr38/Yr17 present in HD2967 and the targeted leaf rust resistance gene LrTrk. Two NILs also showed additional resistance to stripe rust. Therefore, these NILs with rust resistance and an at par yielding ability of H2967 can replace the susceptible cultivar HD2967 to reduce yield losses due to disease.

Drastic shift in flowering phenology of F1 hybrids causing rapid reproductive isolation in Imperata cylindrica in Japan

Abstract Hybridization is a major source of phenotypic variation and a driving force for evolution. Although novel hybrid traits can often disrupt adaptive relationships between the parental phenotypes and their environments, how new hybrid traits disrupt local adaptation remains unclear. Here, we report how a new phenotype of hybrids between two Imperata cylindrica ecotypes contributes to rapid reproductive isolation from their parents and affects hybrid fitness. We analysed 350 accessions of I. cylindrica collected from the 1980s to the 2010s throughout Japan to explore the genetic population structure of the hybrids. We surveyed the flowering periods, seed set, and germination of two ecotypes and their hybrids in both natural habitats and common gardens. Genetic analyses of population structure revealed that the hybrid populations consisted of only F1 individuals, without advanced generation hybrids. The flowering phenology of the F1 plants was delayed until autumn, 5–6 months later than the parental ecotypes. The drastic shift in flowering phenology prevents F1s from backcrossing. In addition, it changes their seed dispersal time to winter. Germination is inhibited by low temperatures, and the seeds likely decay before the next spring, resulting in the absence of an F2 generation. We identified the environmental mismatch of the F1 population as a specific mechanism for the maintenance of an only F1 population. Synthesis. We have demonstrated that this flowering phenology mismatch promotes reproductive isolation between the parents and F1s and affects various temporal components of the hybrids, resulting in a unique hybrid population consisting only of F1s. This system sheds light on the importance of hybrid traits in driving rapid reproductive isolation.

Benzobicyclon efficacy is affected by plant growth stage, HPPD Inhibitor Sensitive 1 (HIS1) expression and zygosity in weedy rice (Oryza sativa)

AbstractBenzobicyclon tolerance in rice (Oryza sativa L.) is dependent on the presence of a functional HIS1 gene, but the level of sensitivity might vary among different cultivars. Greenhouse, laboratory, and field experiments were conducted to further explore the role of HIS1 in cultivated rice tolerance and to exploit findings toward optimizing benzobicyclon activity on weedy rice (unwanted rice; Oryza sativa L.). In a heredity experiment, benzobicyclon tolerance was confirmed to be a semidominant trait conferred by HIS1 based on the intermediate response (ED50 values) of HIS1 heterozygous F1 plants. The spatial–temporal expression of HIS1 was next studied in tissue types (blades, sheaths, and whorls) across tolerant cultivars (‘Roy J’, ‘Diamond’, ‘LaKast’, ‘CLXL745’, and ‘XL753’) and growth stages (2- to 3- compared with 5- to 6-leaf). The relative expression of HIS1 was tissue specific and highest in whorls, followed by blades and then sheaths. Minimal differences in expression across cultivars and growth stages were observed. Furthermore, HIS1 was not largely upregulated at 6 h after benzobicyclon treatment. In the same experiment, cultivar tolerance to benzobicyclon at the label rate of 371 g ha−1 was found to be growth stage dependent. Plant growth was reduced by ∼35% when rice plants were at the 2- to 3- compared with 5- to 6-leaf growth stages. These results show that differences in benzobicyclon tolerance among HIS1 homozygous cultivars is likely not directly correlated with the expression of HIS1. In this research a model was proposed and supported by a field proof of concept study, indicating benzobicyclon efficacy on weedy rice is a function of HIS1 zygosity by growth stage at application. Prior research indicates HIS1 is the dominant allele in weedy rice accessions in Arkansas, and thus, based on our model, benzobicyclon should be applied to weedy rice with ≤2 leaves for suppression.

Expression of heterosis, heterobeltiosis, and gene action in quantitative characters on soybean (Glycine max)

Abstract. Krisnawati A, Adie MM. 2022. Expression of heterosis, heterobeltiosis, and gene action in quantitative characters on soybean (Glycine max). Biodiversitas 23: 1745-1751. Most soybean (Glycine max (L.) Merrill) varieties have been created by crossing two or more parental genotypes. The study aimed to quantify the value of heterosis, heterobeltiosis, the degree of dominance as well as the gene action of the agronomic characters of F1 plants derived from the four soybean cross combinations. All the parents and crosses were evaluated in the screen house of the Indonesian Legume and Tuber Crops Research Institute (Malang, East Java, Indonesia) during 2021. The estimation for mid-parent heterosis (hMP), high-parent heterosis or heterobeltiosis (hHP), degree of dominance, and gene action was done for sevenquantitative characters (plant height, number of branches, number of nodes, number of filled pods, number of empty pods, weight of 10 seeds, and seed yield). The performance of the quantitative characters differs among cross combinations. The estimated value of heterosis mid-parent (hMP) for F1 crosses from four parental combinations ranged from -61.20 to 27.57, heterobeltiosis (hHP) ranged from -71.17 to 9.84, and the degree of dominance ranged from -6.45 to 19.40. The crosses of Derap 1 × Gepak Kuning and Dering 1 × Gepak Kuning showed a positive hMP and hHP for seed yield character. Thus, these hybrids could be used to develop high-yielding varieties with desirable traits in soybean. Seed yield character in the cross of Derap 1 × Gepak Kuning exhibited the overdominance type of gene action, meanwhile, the Dering 1 × Gepak Kuning was incomplete dominance.

Identification of fruit firmness QTL ff2.1 by SLAF-BSA and QTL mapping in melon

Fruit firmness is an important target of melon breeding, as it is associated with shelf life and economic value; however, the precise mechanism that determines fruit firmness during fruit ripening remains elusive. In the present study, one hundred forty-four F2 plants and F2–3 families derived from the high-firmness melon line M2–10 and the low-firmness melon line ZT091 were used to identify major quantitative trait loci by specific-locus amplified fragment sequencing with bulked segregant analysis. Simple sequence repeat (SSR) and cleaved amplified polymorphic sequence (CAPS) markers based on the resequencing of parental lines were also used to narrow the associated region to identify candidate genes. Two regions associated with fruit firmness were investigated, including a 4.87 Mb region on chr. 2 and a 28.7 Mb region on chr. 5 of the melon genome. SSR and CAPS markers were used to construct a genetic map of the associated regions: QTL ff5.1 was located between CmSSR13509 and CmSSR13423 and explained 38.44% of the observed variation, with an LOD threshold of 17.44; ff2.1 was located between CmSSR07709 and SNP22228 and explained 28.14% of the variation, with an LOD threshold of 3.8, and this region included 106 Kb and 10 candidate genes. Quantitative real-time PCR was performed to investigated the investigate candidate gene expression at 15, 20 and 25 days after pollination in the parental lines, and significant expression levels were detected for most of the genes, including four genes of unknown function and MELO3C017519, MELO3C017520, MELO3C017522, MELO3C029506, and MELO3C029520. These results revealed a new QTL, ff2.1, for melon fruit firmness-related gene identification.

Generation mean analysis of important yield traits in Bitter gourd (Momordica charantia)

Generation mean analysis study in bitter gourd was undertaken using six basic generations viz. P1, P2, F1, F2, B1 and B2 population derived from crossing gynoecious line (IIHRBTGy - 491) with two monoecious lines (IIHR Sel -19 -1 and IIHR Sel-78-4). The gynoecious parent was superior for node for first female flowering, number of fruits and yield/plant whereas the monoecious parents were superior for fruit length, fruit diameter and fruit weight. The superior performance of F1 over better parent indicated over-dominance of these traits. F2 plants were significantly diverse. B1 and B2 population exhibited mean value closure to their recurrent parents. Significance of one or more scaling tests, i.e. A, B, C and D in most of the traits revealed the presence of epistasis in both the crosses except for node bearing 1st male flower. Days to 1st female flower opening, node bearing 1st female flower, fruit diameter and yield showed presence of duplicate epistasis whereas days to 1st male flower opening, number of fruits per plant, fruit length and fruit weight showed complimentary epistasis in IIHRBTGy - 491 × IIHR Sel -19 -1 cross. Node bearing 1st female flower, fruit length, fruit diameter and yield showed presence of duplicate epistasis whereas days to 1st female flower opening, days to 1st male flower opening, number of fruits and fruit weight showed complimentary epistasis in IIHRBTGy - 491× IIHR Sel-78-4 cross. Additive gene action may be predominant for inheritance of node bearing 1st male flower.

B-A Chromosome Translocations Possessing an A Centromere Partly Overcome the Root-Restricted Process of Chromosome Elimination in Aegilops speltoides.

Some eukaryotes exhibit dramatic genome size differences between cells of different organs, resulting from the programmed elimination of chromosomes. Aegilops speltoides is an annual diploid species from the Poaceae family, with a maximum number of eight B chromosomes (Bs) in addition to its inherent seven pairs of standard A chromosomes (As). The Bs of this species undergo precise elimination in roots early in embryo development. In areal parts of the plant, the number of Bs is stable. To affect the root restricted process of B chromosome elimination, we employed X-ray mutagenesis, and different types of restructured Bs were identified. Standard Bs were observed in all analyzed shoots of mutagenized plants, while B-A translocations were only observed in 35.7% of F1 plants. In total 40 different B variants inconsistently escaped the elimination process in roots. As a result, mosaicism of B chromosome variants was found in roots. Only a small B chromosome fragment fused to an A chromosome was stably maintained in roots and shoots across F1 to F3 generations. The absence of B-A translocation chromosomes possessing a derived B centromere in root cells implies that the centromere of the B is a key component of the chromosome elimination process.

A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple

IntroductionGenomic heterozygosity, self-incompatibility, and rich-in somatic mutations hinder the molecular breeding efficiency of outcrossing plants. ObjectivesWe attempted to develop an efficient integrated strategy to identify quantitative trait loci (QTLs) and trait-associated genes, to develop gene markers, and to construct genomics-assisted prediction (GAP) modes. MethodsA novel protocol, bulked segregant analysis tool for out-crossing species (BSATOS), is presented here, which is characterized by taking full advantage of all segregation patterns (including AB × AB markers) and haplotype information. To verify the effectiveness of the protocol in dealing with the complex traits of outbreeding species, three apple cross populations with 9,654 individuals were adopted. ResultsBy using BSATOS, 90, 60, and 77 significant QTLs were identified successfully and candidate genes were predicted for apple fruit weight (FW), fruit ripening date (FRD), and fruit soluble solid content (SSC), respectively. The gene-based markers were developed and genotyped for 1,396 individuals in a training population, including 145 Malus accessions and 1,251 F1 plants of the three full-sib families. GAP models were trained using marker genotype effect estimates of the training population. The prediction accuracy was 0.7658, 0.6455, and 0.3758 for FW, FRD, and SSC, respectively. ConclusionThe BSATOS and GAP models provided a convenient and efficient methodology for candidate gene mining and molecular breeding in out-crossing plant species. The BSATOS pipeline can be freely downloaded from: https://github.com/maypoleflyn/BSATOS.

A combinatorial strategy to identify various types of QTLs for quantitative traits using extreme phenotype individuals in an F2 population

Theoretical and applied studies demonstrate the difficulty of detecting extremely over-dominant and small-effect genes for quantitative traits via bulked segregant analysis (BSA) in an F2 population. To address this issue, we proposed an integrated strategy for mapping various types of quantitative trait loci (QTLs) for quantitative traits via a combination of BSA and whole-genome sequencing. In this strategy, the numbers of read counts of marker alleles in two extreme pools were used to predict the numbers of read counts of marker genotypes. These observed and predicted numbers were used to construct a new statistic, Gw, for detecting quantitative trait genes (QTGs), and the method was named dQTG-seq1. This method was significantly better than existing BSA methods. If the goal was to identify extremely over-dominant and small-effect genes, another reserved DNA/RNA sample from each extreme phenotype F2 plant was sequenced, and the observed numbers of marker alleles and genotypes were used to calculate Gw to detect QTGs; this method was named dQTG-seq2. In simulated and real rice dataset analyses, dQTG-seq2 could identify many more extremely over-dominant and small-effect genes than BSA and QTL mapping methods. dQTG-seq2 may be extended to other heterogeneous mapping populations. The significance threshold of Gw in this study was determined by permutation experiments. In addition, a handbook for the R software dQTG.seq, which is available at https://cran.r-project.org/web/packages/dQTG.seq/index.html, has been provided in the supplemental materials for the users’ convenience. This study provides a new strategy for identifying all types of QTLs for quantitative traits in an F2 population.

Marker assisted selection and segregation distortion studies in rice (Oryza sativa)

Rice (Oryza sativa L.) is an important staple food crop and is grown across different regions and moisture regimesacross Asian countries. The present study was carried out during rainy (kharif) season 2017–19 for introgressinggenes, raising F1 plants, evaluation of F2 plants and marker distortion studies at Marker Assisted Selection Laboratory, University of Agricultural sciences, Bangalore. True F1 plants were confirmed using polymorphic SSR marker RM242 and selfed to develop F2 plants. Marker assisted identification using 11 trait specific SSR markers linked to higher contributing alleles for drought, blast and bacterial leaf blight (BLB) resistance in F2 population was derived from a japonica variety Moroberekan and indica variety IR 64. F2 population exhibited highly significant segregation distortions for four (36.4%) out of 11 SSR markers. Out of four distorted markers, RM242 and RM235 were towards IR64 (male parent) and RM11943 and RM243 distorted towards heterozygote and Moroberekan (female parent), respectively. The allele frequency and distribution of genotype frequencies in the F2 population were analyzed for SSR markers, to find out factors that attributed to segregation distortion. Three markers (RM11943, RM243 and RM235) showed distorted allele frequency, with normal genotype frequency and one showed distorted genotype frequency with normal allele frequency, which indicates that these markers were influenced at gametic and zygotic level, respectively.

The Memory of Rice Response to Spaceflight Stress: From the Perspective of Metabolomics and Proteomics.

The stress response of plants to spaceflight has been confirmed in contemporary plants, and plants retained the memory of spaceflight through methylation reaction. However, how the progeny plants adapt to this cross-generational stress memory was rarely reported. Here, we used the ShiJian-10 retractable satellite carrying Dongnong416 rice seeds for a 12.5-day on-orbit flight and planted the F2 generation after returning to the ground. We evaluated the agronomic traits of the F2 generation plants and found that the F2 generation plants had no significant differences in plant height and number of tillers. Next, the redox state in F2 plants was evaluated, and it was found that the spaceflight broke the redox state of the F2 generation rice. In order to further illustrate the stress response caused by this redox state imbalance, we conducted proteomics and metabolomics analysis. Proteomics results showed that the redox process in F2 rice interacts with signal transduction, stress response, and other pathways, causing genome instability in the plant, leading to transcription, post-transcriptional modification, protein synthesis, protein modification, and degradation processes were suppressed. The metabolomics results showed that the metabolism of the F2 generation plants was reshaped. These metabolic pathways mainly included amino acid metabolism, sugar metabolism, cofactor and vitamin metabolism, purine metabolism, phenylpropane biosynthesis, and flavonoid metabolism. These metabolic pathways constituted a new metabolic network. This study confirmed that spaceflight affected the metabolic changes in offspring rice, which would help better understand the adaptation mechanism of plants to the space environment.

Unraveling the genetic components of perenniality: Toward breeding for perennial grains

Social Impact StatementAlthough tremendously successful at feeding humanity, row crop agriculture based on annuals contributes to numerous ecosystem dis‐services, ranging from soil degradation and aquatic eutrophication to greenhouse gas production. In contrast, perennial grain crops (which produce harvests for multiple seasons from single plantings) have the potential to provide valuable regulating and supporting ecosystem services in addition to food production. In particular, losses of ecological capital that threaten permanent food insecurity such as ~1% of global soil per year are expected to be mitigated or even reversed by crops that combine the high yield realized by scientific breeding via multiple cropping cycles from single plantings.Summary Perennial herbaceous may provide food and biomass while preserving ecological capital and reducing energy inputs. Sorghum has two perennial relatives and rich morphological diversity being used to breed for perenniality. We elucidate genetic determinants of rhizomatousness and survival, in two BC1F2 populations totaling 246 genotypes derived from backcrossing different annual Sorghum bicolor X perennial S. halepense F1 plants to a tetraploidized S. bicolor. RNA‐seq assisted in identifying candidate genes for rhizomatousness. Correspondence of rhizomatousness quantitative trait loci (QTLs) with those from two populations derived from crosses between S. halepense progenitors S. bicolor X S. propinquum suggests either the preservation of interspecific polymorphism or the formation of novel alleles following polyploid S. halepense formation. Correspondence of tillering and branching QTLs further supports their developmental. Identification of genes from RNA‐seq study within QTL intervals provides insight toward discovery of causal rhizomatous genes. An unexpected finding from both S. halepense‐ and S. propinquum‐derived populations is that alleles contributing to late flowering are related to reduced rhizomatousness. Twelve of 16 QTL regions conferring rhizomatousness fall in paleo‐duplicated regions tracing to single ancestral regions 96 million years ago, indicating that corresponding genes in these regions have retained similar functions since the duplication event.