F2 Population Research Articles

Agronomic performance and phenotypic variability of the F2 population derived from various types of okra varieties

Abstract Okra is a functional vegetable with high nutrient content and medicinal value potential. Evaluating genetic material from various genetic sources is a standard procedure in plant breeding programs. A field study was carried out to evaluate the agronomic traits of F2 populations derived from various types of varieties and assess the phenotypic variability of the traits. The research was conducted at the Research Station of the Faculty of Agriculture, Andalas University, from January to May 2021. The materials used are seeds from self-pollinated of 16 F1 populations with various varieties, i.e., hybrid, composite, introduced and local varieties. Data was collected based on an individual observation, and the data were then analyzed using descriptive statistics. Results showed that the entire population of the F2 derived from both hybrid or composite varieties, introduced or local varieties, has diverse agronomic traits, indicating their potential to be developed as parental inbred lines. All agronomic traits evaluated showed wide variability, indicating a high possibility to obtain plants with valuable and desirable traits. The exception was found for the optimum picking time; however, the optimum picking time 7, 8 or 9 DAA is sufficient to obtain fruit with higher fruit weight and fruit size.

Reproducible Quantitative Trait Loci for Resistance to Soft Rot Caused by Dickeya dianthicola Derived from the Wild Potato Solanum microdontum (PI 458355) Are Located on Chromosomes 1, 3, and 5.

The potato wild relative Solanum microdontum is a breeder-friendly source of genetic resistance to soft rot. Our objectives were to (i) identify loci associated with soft rot resistance in S. microdontum germplasm and (ii) develop bi-parental populations in a self-compatible S. tuberosum genetic background to recover segregating F2 progenies, construct a linkage map, and identify quantitative trait loci (QTLs). Under objective (i), tubers from 103 S. microdontum genotypes from the United States Potato Genebank were inoculated with a high virulence strain of Dickeya dianthicola, and lesion size was measured after a 24-h incubation period at 30°C. Association analysis using 3,490 polymorphic Infinium array SNP markers identified soft rot resistance loci on chromosomes 1, 2, 3, 5, 7, 8, 11, and 12. Under objective (ii), a resistant S. microdontum accession PI 458355 was crossed with a highly fertile, self-compatible, diploid S. tuberosum pollen parent (PI 654351) to generate segregating F2 populations. Composite interval mapping was conducted using a genetic linkage map with 970 GBS-based SNP markers. Reproducible QTLs were detected on chromosomes 1, 3, and 5, explaining 11, 13, and 23% of the phenotypic variation, respectively. Homozygous S. microdontum alleles at the QTL on chromosome 5 and heterozygous or homozygous S. microdontum alleles at QTLs on chromosomes 1 and 3 significantly decrease lesion size compared with the homozygous S. tuberosum parent. The germplasm created in these studies provides a resource for studying traits from S. microdontum, and we can use the advanced F2 selections for future potato improvement. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A 5.2-kb insertion in the coding sequence of PavSCPL, a serine carboxypeptidase-like enhances fruit firmness in Prunus avium.

Fruit firmness is an important trait in sweet cherry breeding because it directly positively influences fruit transportability, storage and shelf life. However, the underlying genes responsible and the molecular mechanisms that control fruit firmness remain unknown. In this study, we identified a candidate gene, PavSCPL, encoding a serine carboxypeptidase-like protein with natural allelic variation, that controls fruit firmness in sweet cherry using map-based cloning and functionally characterized PavSCPL during sweet cherry fruit softening. Genetic analysis revealed that fruit firmness in the 'Rainier' × 'Summit' F1 population was controlled by a single dominant gene. Bulked segregant analysis combined with fine mapping narrowed the candidate gene to a 473-kb region (7418778-7 891 914 bp) on chromosome 6 which included 72 genes. The candidate gene PavSCPL, and a null allele harbouring a 5244-bp insertion in the second exon that completely inactivated PavSCPL expression and resulted in the extra-hard-flesh phenotype, were identified by RNA-sequencing analysis and gene cloning. Quantitative RT-PCR analysis revealed that the PavSCPL expression level was increased with fruit softening. Virus-induced gene silencing of PavSCPL enhanced fruit firmness and suppressed the activities of certain pectin-degrading enzymes in the fruit. In addition, we developed functional molecular markers for PavSCPL and the Pavscpl5.2-k allele that co-segregated with the fruit firmness trait. Overall, this research identified a crucial functional gene for fruit firmness. The results provide insights into the genetic control and molecular mechanism of the fruit firmness trait and present useful molecular markers for molecular-assisted breeding for fruit firmness in sweet cherry.

High-resolution bulked segregant analysis enables candidate gene identification for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.).

Bacterial wilt, caused by Xanthomonas translucens pv. graminis (Xtg), is a serious disease of economically important forage grasses, including Italian ryegrass (Lolium multiflorum Lam.). A major QTL for resistance to Xtg was previously identified, but the precise location as well as the genetic factors underlying the resistance are yet to be determined. To this end, we applied a bulked segregant analysis (BSA) approach, using whole-genome deep sequencing of pools of the most resistant and most susceptible individuals of a large (n = 7484) biparental F2 population segregating for resistance to Xtg. Using chromosome-level genome assemblies as references, we were able to define a ~300 kb region highly associated with resistance on pseudo-chromosome 4. Further investigation of this region revealed multiple genes with a known role in disease resistance, including genes encoding for Pik2-like disease resistance proteins, cysteine-rich kinases, and RGA4- and RGA5-like disease resistance proteins. Investigation of allele frequencies in the pools and comparative genome analysis in the grandparents of the F2 population revealed that some of these genes contain variants with allele frequencies that correspond to the expected heterozygosity in the resistant grandparent. This study emphasizes the efficacy of combining BSA studies in very large populations with whole genome deep sequencing and high-quality genome assemblies to pinpoint regions associated with a binary trait of interest and accurately define a small set of candidate genes. Furthermore, markers identified in this region hold significant potential for marker-assisted breeding strategies to breed resistance to Xtg in Italian ryegrass cultivars more efficiently.

Mapping and Detection of Genes Related to Trichome Development in Black Gram (Vigna mungo (L.) Hepper).

Black gram (Vigna mungo (L.) Hepper) is a pulses crop with good digestible protein and a high carbohydrate content, so it is widely consumed as human food and animal feed. Trichomes are large, specialized epidermal cells that confer advantages on plants under biotic and abiotic stresses. Genes regulating the development of trichomes are well characterized in Arabidopsis and tomato. However, little is known about trichome development in black gram. In this study, a high-density map with 5734 bin markers using an F2 population derived from a trichome-bearing and a glabrous cultivar of black gram was constructed, and a major quantitative trait locus (QTL) related to trichomes was identified. Six candidate genes were located in the mapped interval region. Fourteen single-nucleotide polymorphisms (SNPs) or insertion/deletions (indels) were associated with those genes. One indel was located in the coding region of the gene designated as Scaffold_9372_HRSCAF_11447.164. Real-time quantitative PCR (qPCR) analysis demonstrated that only one candidate gene, Scaffold_9372_HRSCAF_11447.166, was differentially expressed in the stem between the two parental lines. These two candidate genes encoded the RNA polymerase-associated protein Rtf1 and Bromodomain adjacent to zinc finger domain protein 1A (BAZ1A). These results provide insights into the regulation of trichome development in black gram. The candidate genes may be useful for creating transgenic plants with improved stress resistance and for developing molecular markers for trichome selection in black gram breeding programs.

Unveiling the molecular regulatory mechanisms underlying sucrose accumulation and oil reduction in peanut kernels through genetic mapping and transcriptome analysis

Sucrose content is a key factor for the flavor of edible peanut, which determines the sweet taste of fresh peanut and also attribute to pleasant flavor of roasted peanut. To explore the genetic mechanism of the sucrose content in peanut, an F2 population was created by crossing the sweet cultivar Zhonghuatian 1 (ZHT1) with Nanyangbaipi (NYBP). A genomic region spanning 28.26 kb on chromosome A06 was identified for the sucrose content through genetic mapping, elucidating 47.5% phenotypic variance explained. As the sucrose content had a significantly negative correlation with the oil content, this region was also found to be related to the oil content explaining 37.2% of phenotype variation. In this region, Arahy.42CAD1 was characterized as the most likely candidate gene through a comprehensive analysis. The nuclear localization of Arahy.42CAD1 suggests its potential involvement in the regulation of gene expression for sucrose and oil contents in peanut. Transcriptome analysis of the developing seeds in both parents revealed that genes involved in glycolysis and triacylglycerol biosynthesis pathways were not significantly down-regulated in ZHT1, indicating that the sucrose accumulation was not attributed to the suppression of triacylglycerol biosynthesis. Based on the WGCNA analysis, Arahy.42CAD1 was co-expressed with the genes involved in vesicle transport and oil body assembly, suggesting that the sucrose accumulation may be caused by disruptions in TAG transportation or storage mechanisms. These findings offer new insights into the molecular mechanisms governing sucrose accumulation in peanut, and also provide a potential gene target for enhancing peanut flavor.

Identification of Clubroot (Plasmodiophora brassicae) Resistance Loci in Chinese Cabbage (Brassica rapa ssp. pekinensis) with Recessive Character.

The soil-borne pathogen Plasmodiophora brassicae is the causal agent of clubroot, a major disease in Chinese cabbage (Brassica rapa ssp. pekinensis). The host's resistance genes often confer immunity to only specific pathotypes and may be rapidly overcome. Identification of novel clubroot resistance (CR) from germplasm sources is necessary. In this study, Bap246 was tested by being crossed with different highly susceptible B. rapa materials and showed recessive resistance to clubroot. An F2 population derived from Bap246 × Bac1344 was used to locate the resistance Quantitative Trait Loci (QTL) by Bulk Segregant Analysis Sequencing (BSA-Seq) and QTL mapping methods. Two QTL on chromosomes A01 (4.67-6.06 Mb) and A08 (10.42-11.43 Mb) were found and named Cr4Ba1.1 and Cr4Ba8.1, respectively. Fifteen and eleven SNP/InDel markers were used to narrow the target regions in the larger F2 population to 4.67-5.17 Mb (A01) and 10.70-10.84 Mb (A08), with 85 and 19 candidate genes, respectively. The phenotypic variation explained (PVE) of the two QTL were 30.97% and 8.65%, respectively. Combined with gene annotation, mutation site analysis, and real-time quantitative polymerase chain reaction (qRT-PCR) analysis, one candidate gene in A08 was identified, namely Bra020861. And an insertion and deletion (InDel) marker (co-segregated) named Crr1-196 was developed based on the gene sequence. Bra013275, Bra013299, Bra013336, Bra013339, Bra013341, and Bra013357 in A01 were the candidate genes that may confer clubroot resistance in Chinese cabbage. The resistance resource and the developed marker will be helpful in Brassica breeding programs.

Fine-Tuning Quantitative Trait Loci Identified in Immortalized F2 Population Are Essential for Genomic Prediction of Hybrid Performance in Maize

Maize breeding is greatly affected by hybrid vigor, a phenomenon that hybrids exhibit superior performance than parental lines. The immortalized F2 population (IMF2) is ideal for the genetic dissection and prediction of hybrid performance. Here, in this study, we conducted the QTL mapping and genomic prediction of six traits related to plant architecture using an IMF2 population. Broad-sense heritability of these traits ranged from 0.85 to 0.94. Analysis of genetic effects showed that additive variance was the main contributor to phenotypic variations. The mapping of quantitative trait loci (QTLs) revealed 10 to 16 QTLs (including pleiotropic loci and epistatic QTLs) for the six traits. Additionally, we identified 15 fine-tuning QTLs for plant height (PH). For genomic prediction (GP), the model of additive and dominance (AD) exhibited higher prediction accuracy than those fitting general combining ability (GCA) and its combination with special combining ability (SCA) effects for all tested traits. And adding the epistasis (E) effect into the AD model did not significantly increase its prediction accuracy. Moreover, the identified 15 fine-tuning QTLs of PH, which exerted large genomic prediction effects, were verified by the marker effect of GP. Our results not only provide an approach for the fine-mapping of fine-tuning QTLs but also serve as references for GP breeding in crops.

Evaluation of downy mildew resistance in spinach (Spinacia oleracea)

Spinach (Spinacia oleracea) is an economically important leafy vegetable grown in the United States and world-wide. The downy mildew pathogen, Peronospora effusa (Pfs), is a major biotic constraint impacting spinach production and quality. The use of resistant cultivars is an economical and environmentally-friendly management option especially in organic production systems. As new races of the pathogen continue to appear, there is a need to continue to select for resistance to the emerging races. The objectives of this study were to evaluate a set of spinach hybrids and F2 breeding populations for resistance to Pfs race 5 to develop a better understanding of the genetics of downy mildew resistance. Also, we screened 39 commercial spinach cultivars for resistance to a recently identified race, Pfs race 19. The genetics of resistance to Pfs 5 was determined by greenhouse inoculations of F1 progeny (individual crosses between near isogenic lines, NIL3 or NIL1 and susceptible genotype, Viroflay) and F2 population progeny (cross between Califlay and susceptible Viroflay). Two hybrids were examined for resistance to Pfs 5. The results indicated that resistance conferred at the RPF1 or the RPF3 loci in a heterozygous (Rr) condition to Pfs 5 was completely dominant. Also, Chi-square analysis of the segregation pattern in the F2 population showed that resistance to Pfs race 5 was conferred by a single dominant gene. A total of 22 out of 39 spinach commercial cultivars were resistant to the newly reported Pfs race 19 and could be used in breeding programs to develop new cultivars with resistance to Pfs 19.

Fine mapping of ClLOX, a QTL for powdery mildew resistance in watermelon (Citrullus lanatus L.).

ClLOX, is located on chromosome 2 and encodes a lipoxygenase gene, which induced watermelon powdery mildew resistance by inhibiting pathogen spread. Powdery mildew is one of the most severe fungal diseases reducing yield and quality of watermelon (Citrullus lanatus L.) and other cucurbit crops. Genes responsible for powdery mildew resistance in watermelon are highly valuable. In this study, we first identified the QTL pm-lox for powdery mildew resistance in watermelon, located within a 0.93Mb interval of chromosome 2, via XP-GWAS method using two F2 populations. The F2:3 families from one of the F2 populations were then used for fine-mapping the pm-lox locus into a 9,883bp physical region between 29,581,906 and 29,591,789, containing only two annotated genes. Of these, only ClG42_02g0161300 showed a significant differential expression between the resistant and susceptible lines after powdery mildew inoculation based on RNA sequencing (RNA-seq) and qRT-PCR analysis, and is designated ClLOX. Derived Cleaved Amplified Polymorphic Sequence (dCAPs) markers were developed and validated. In addition, our tests showed that the resistance was anti-spread rather than anti-infection of the pathogen. This study identified a new resistance gene (ClLOX), provided insights into the mechanism of powdery mildew resistance, and developed a molecular marker for watermelon breeding.

OcBSA: An NGS-based bulk segregant analysis tool for outcross populations

Constructing inbred lines for self-incompatible species and species with long generation times is challenging, making the use of F1 outcross/segregating populations the main strategy for genetic studies of such species. However, there is a lack of dedicated algorithms/tools for rapid quantitative trait locus (QTL) mapping using the F1 populations. To this end, we have designed and developed an algorithm/tool called OcBSA specifically for QTL mapping of F1 populations. OcBSA transforms the four-haplotype inheritance problem from the two heterozygous diploid parents of the F1 population into the two-haplotype inheritance problem common in current genetic studies by removing the two haplotypes from the heterozygous parent that do not contribute to phenotype segregation in the F1 population. Testing of OcBSA on 1800 simulated F1 populations demonstrated its advantages over other currently available tools in terms of sensitivity and accuracy. In addition, the broad applicability of OcBSA was validated by QTL mapping using seven reported F1 populations of apple, pear, peach, citrus, grape, tea, and rice. We also used OcBSA to map the QTL for flower color in a newly constructed F1 population of potato generated in this study. The OcBSA mapping result was verified by the insertion or deletion markers to be consistent with a previously reported locus harboring the ANTHOCYANIN 2 gene, which regulates potato flower color. Taken together, these results highlight the power and broad utility of OcBSA for QTL mapping using F1 populations and thus a great potential for functional gene mining in outcrossing species. For ease of use, we have developed both Windows and Linux versions of OcBSA, which are freely available at: https://gitee.com/Bioinformaticslab/OcBSA.

Linkage map construction and QTL identification for yield related traits of rice (Oryza sativa L.)

The study was undertaken to construct a linkage map and to identify the QTLs for heading date, plant height, and culm strength using a F2 population derived from Ayeyarmin/IR 64, two varieties distinctly different in heading date and plant height. A total of 233 F2 individuals were genotyped using 70 SSR primers, and phenotypic data were collected for heading date, plant height and culm strength traits. Fifty-four out of 70 marker loci were mapped across twelve rice chromosomes spanning a total map length of 1592.30 cM with an average distance of 29.49 cM between adjacent marker loci using MAPMAKER/EXP 3. Composite interval mapping for QTL analysis was conducted with 1000 permutation time at 0.05 probability level using WinQTL Cartographer version 2.5. One major QTL for heading date was mapped between marker RM204 and RM50 on chromosome 6. One major QTL for culm strength was mapped between marker RM1003-RM5931, and two major QTLs for plant height were mapped between RM84-RM1003 and RM1003-RM5931 on chromosome 1. The molecular markers linked to the major QTLs could be potentially used in marker-assisted selection for the rainfed rice improvement breeding program.

Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice

Bulked-segregant analysis by deep sequencing (BSA-seq) is a widely used method for mapping QTL (quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2 populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F3 populations offering notable advantages over F2 populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading (DTH) in a 7200-plant rice F3 population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F3 populations and multi-environment experiments can achieve high power, resolution, and reliability.

Map-based cloning of qLPA01.1, a favorable allele from the Gossypium tomentosum chromosome segment line

Cotton is an important natural fiber crop worldwide which plays a vital role in our daily life. High yield is a constant goal of cotton breeding, and lint percentage (LP) is one of the important components of cotton fiber yield. A stable QTL controlling LP, qLPA01.1, was identified on chromosome A01 from Gossypium hirsutum introgressed lines with G. tomentosum chromosome segments in a previous study. To fine-map qLPA01.1, an F2 population with 986 individuals was established by crossing G. hirsutum cultivar CCRI35 with the chromosome segment substitution line HT_390. A high-resolution genetic map including 47 loci and spanning 56.98 cM was constructed in the QTL region, and qLPA01.1 was ultimately mapped into an interval corresponding to an ~80 kb genome region of chromosome A01 in the reference genome, which contained six annotated genes. Transcriptome data and sequence analysis revealed that S-acyltransferase protein 24 (GoPAT24) might be the target gene of qLPA01.1. This result provides the basis for cotton fiber yield improvement via marker-assisted selection (MAS) and further studies on the mechanism of cotton fiber development.

Aphid Resistance Segregates Independently of Cardenolide and Glucosinolate Content in an Erysimum cheiranthoides (Wormseed Wallflower) F2 Population.

Plants in the genus Erysimum produce both glucosinolates and cardenolides as a defense mechanism against herbivory. Two natural isolates of Erysimum cheiranthoides (wormseed wallflower) differed in their glucosinolate content, cardenolide content, and their resistance to Myzus persicae (green peach aphid), a broad generalist herbivore. Both classes of defensive metabolites were produced constitutively and were not further induced by aphid feeding. To investigate the relative importance of glucosinolates and cardenolides in E. cheiranthoides defense, we generated an improved genome assembly, genetic map, and segregating F2 population. The genotypic and phenotypic analysis of the F2 plants identified quantitative trait loci, which affected glucosinolates and cardenolides, but not the aphid resistance. The abundance of most glucosinolates and cardenolides was positively correlated in the F2 population, indicating that similar processes regulate their biosynthesis and accumulation. Aphid reproduction was positively correlated with glucosinolate content. Although the overall cardenolide content had little effect on aphid growth and survival, there was a negative correlation between aphid reproduction and helveticoside abundance. However, this variation in defensive metabolites could not explain the differences in aphid growth on the two parental lines, suggesting that processes other than the abundance of glucosinolates and cardenolides have a predominant effect on aphid resistance in E. cheiranthoides.

Combining Image-Based Phenotyping and Multivariate Analysis to Estimate Fruit Fresh Weight in Segregation Lines of Lowland Tomatoes

The fruit weight is an important guideline for breeders and farmers to increase marketable productions, although conventionally it requires destructive measurements. The combination of image-based phenotyping (IBP) approaches with multivariate analysis has the potential to further improve the line selection based on economical trait, like fruit weight. Therefore, this study aimed to evaluate the potential of image-derived phenotypic traits as proxies for individual fruits weight estimation using multivariate analysis. To this end, an IBP experimentation was carried out on five populations of low-land tomato. Specifically, the Mawar (M; 10 plants), Karina (K; 10 plants), and F2 generation cross (100 lines) samples were used to extract training data for the proposed estimation model, while data derived from M/K//K backcross population (35 lines) and F5 population (50 lines) plants were used for destructive and non-destructive validation, respectively. Several phenotypic traits were extracted from each imaged tomato fruit, including the slice and whole fruit area (FA), round (FR), width (FW), height (FH), and red (RI), green (GI) and blue index (BI), and used as inputs of a genetic- and multivariate-based method for non-destructively predicting its fresh weight (FFW). Based on this research, the whole FA has the greatest potential in predicting tomato FFW regardless to the analyzed cultivar. The relevant model exhibited high power in predicting FFW, as explained by R2-adjusted, R2-deviation and RMSE statistics obtained for calibration (81.30%, 0.20%, 3.14 g, respectively), destructive (69.80%, 0.90%, 4.46 g, respectively) and non-destructive validation (80.20%, 0.50%, 2.12 g, respectively). These results suggest the potential applicability of the proposed IBP approach in guiding field robots or machines for precision harvesting based on non-destructive estimations of fruit weight from image-derived area, thereby enhancing agricultural practices in lowland tomato cultivation.

Freezing stress response of wild and cultivated chickpeas.

Chickpea is an economically and nutritionally important grain legume globally, however, cold stress has adverse effects on its growth. In cold countries, like Canada where the growing season is short, having cold stress-tolerant varieties is crucial. Crop wild relatives of chickpea, especially Cicer reticulatum, can survive in suboptimal environments and are an important resource for crop improvement. In this study, we explored the performance of eleven C. reticulatum wild accessions and two chickpea cultivars, CDC Leader and CDC Consul, together with a cold sensitive check ILC533 under freezing stress. Freezing tolerance was scored based on a 1-9 scale. The wild relatives, particularly Kesen_075 and CudiA_152, had higher frost tolerance compared to the cultivars, which all died after frost treatment. We completed transcriptome analysis via mRNA sequencing to assess changes in gene expression in response to freezing stress and identified 6,184 differentially expressed genes (DEGs) in CDC Consul, and 7,842 DEGs in Kesen_075. GO (gene ontology) analysis of the DEGs revealed that those related to stress responses, endogenous and external stimuli responses, secondary metabolite processes, and photosynthesis were significantly over-represented in CDC Consul, while genes related to endogenous stimulus responses and photosynthesis were significantly over-represented in Kesen_075. These results are consistent with Kesen_075 being more tolerant to freezing stress than CDC Consul. Moreover, our data revealed that the expression of CBF pathway-related genes was impacted during freezing conditions in Kesen_075, and expression of these genes is believed to alleviate the damage caused by freezing stress. We identified genomic regions associated with tolerance to freezing stress in an F2 population derived from a cross between CDC Consul and Kesen_075 using QTL-seq analysis. Eight QTLs (P<0.05) on chromosomes Ca3, Ca4, Ca6, Ca7, Ca8, and two QTLs (P<0.01) on chromosomes Ca4 and Ca8, were associated with tolerance to freezing stress. Interestingly, 58 DEGs co-located within these QTLs. To our knowledge, this is the first study to explore the transcriptome and QTLs associated with freezing tolerance in wild relatives of chickpea under controlled conditions. Altogether, these findings provide comprehensive information that aids in understanding the molecular mechanism of chickpea adaptation to freezing stress and further provides functional candidate genes that can assist in breeding of freezing-stress tolerant varieties.

Screening and Resistance Locus Identification of the Mutant fcrZ22 Resistant to Crown Rot Caused by Fusarium pseudograminearum.

Crown rot caused by Fusarium pseudograminearum is a devastating wheat disease worldwide. In addition to yield losses, the fungi causing Fusarium crown rot (FCR) also deteriorate the quality and safety of food because of the production of mycotoxins. Planting resistant cultivars is an effective way to control FCR. However, most wheat cultivars are susceptible to FCR. Therefore, development of new sources and detection of loci for FCR resistance are necessary. In the present study, a resistant mutant, fcrZ22, was identified from an ethyl methane sulfonate (EMS)-mutagenized population of the cultivar Zhoumai 22, and then fcrZ22 was crossed with the wild type to produce an F2 population. Genetic analysis of the F2 population was carried out by the mixed inheritance model of major genes plus polygenes, and 20 resistant and 20 susceptible plants were selected to assemble mixed pools. Combining 660K SNP arrays, the resistance loci were detected by bulked segregant analysis. The resistance to FCR caused by F. pseudograminearum in the F2 population was in accordance with the "mixed model with two major genes of additive-epistasis effect + additive-dominant polygenes," and the heritability of the major gene was 0.92. Twenty-one loci were detected, which were located on 10 chromosomes, namely, 1B (1), 1D (1), 2A (3), 1B (1), 3A (3), 3B (3), 4A (2), 5A (2), 7A (3), and 7B (2). Among the 21 loci, eight were new loci for FCR resistance. This is the first report of detecting loci for FCR resistance from a mutant. The results of the present study provided excellent germplasm resources for breeding wheat cultivars with FCR resistance and laid the foundation for fine mapping of FCR resistance loci.

Genotype and phenotype diversity of the F2 population three-way cross soybean (Glycine max [L.] Merrill) results

Increasing soybean production through plant crossing helps to supply soybean needs. Three-way crossing of three parents, Grobogan, Anjasmoro, and Dega 1 is expected to increase soybean productivity. Interbreeding is an effort to form a basic population to increase genetic diversity. Based on this, this study aims to determine the diversity of genotypes and phenotypes of the F2 population resulting from a cross between three soybean parents [Glycine max (L.) Merrill]. This research was conducted on Tanjung Selamat Village, Sunggal District, Deli Serdang Regency land. Observations were made by observing all plant populations in the field. Characters observed include plant height, flowering age, number of primary branches, and harvest age. The results showed that the diversity of genotypes and phenotypes of the F2 population varied, this was based on the highest standard deviation value in the F2 population compared to the 3 parent soybean plants. The plant height character has a high diversity value based on the KKG and KKF values.

Identification of QTLs associated with very-long chain fatty acid (VLCFA) content via linkage mapping and BSA-seq in peanut.

Three major QTLs qA01, qB04.1 and qB05 for VLCFA content and their corresponding allele-specific markers will benefit peanut low VLCFA breeding, and a candidate gene Arahy.IF1JV3 was predicted. Peanut is a globally significant oilseed crop worldwide, and contains a high content (20%) of saturated fatty acid (SFA) in its seeds. As high level SFA intake in human dietary may increase the cardiovascular disease risk, reducing the SFA content in peanut is crucial for improving its nutritional quality. Half of the SFAs in peanut are very long-chain fatty acids (VLCFA), so reducing the VLCFA content is a feasible strategy to decrease the total SFA content. Luoaowan with extremely low VLCFA (4.80%) was crossed with Jihua16 (8.00%) to construct an F2:4 population. Three major QTLs including qA01, qB04.1 and qB05 for VLCFA content were detected with 4.43 ~ 14.32% phenotypic variation explained through linkage mapping. Meanwhile, three genomic regions on chromosomes B03, B04 and B05 were identified via BSA-seq approach. Two co-localized intervals on chromosomes B04 (100.10 ~ 103.97Mb) and B05 (6.39 ~ 10.90Mb) were identified. With markers developed based on SNP/InDel variations in qA01 between the two parents, the remaining interval was refined to 103.58 ~ 111.14Mb. A candidate gene Arahy.IF1JV3 encoding a β-ketoacyl-CoA synthase was found in qA01, and its expression level in Luoaowan was significantly lower than that in Jihua16. Allele-specific markers targeting qA01, qB04.1 and qB05 were developed and validated in F4 population, and an elite line with high oleic, low VLCFA (5.05%) and low SFA (11.48%) contents was selected. This study initially revealed the genetic mechanism of VLCFA content, built a marker-assisted selection system for low VLCFA breeding, and provided an effective method to decrease the SFA content in peanut.