Characterization of AFLP Markers Associated with Growth in the Kuruma Prawn, <Emphasis Type="Italic">Marsupenaeus japonicus</Emphasis>, and Identification of a Candidate Gene

Growth rate of the Kuruma prawn, Marsupenaeus japonicus is an important economic trait, with larger animals commanding higher market prices. To identify gene markers associated with growth, a genetic map of a full-sib F₂ intercross family of M. japonicus has previously been generated and quantitative trait loci (QTL) influencing weight, total length, and carapace length were identified. In this study, amplified fragment length polymorphism (AFLP) markers associated with the major QTL region, contributing 16% to phenotypic variation, were characterized. Flanking sequence has been obtained and allelic variants responsible for segregation patterns of these markers have been identified. The genomic sequence surrounding the AFLP band 7.21a, residing under the QTL peak, contains a gene sequence homologous to the elongation of very long chain fatty acids-like (ELOVL) protein family. A full-length mRNA (ELOVL-MJ) encoding this protein was isolated from M. japonicus, representing both the first ELOVL gene in crustacea and the first candidate gene identified via QTL studies in crustacea.     

Identification of QTLs for Yield and Associated Traits in F₂ Population of Rice

Identification of quantitative trait loci (QTLs) controlling yield and yield-related traits in rice was performed in the F₂ mapping population derived from parental rice genotypes DHMAS and K343. A total of 30 QTLs governing nine different traits were identified using the composite interval mapping (CIM) method. Four QTLs were mapped for number of tillers per plant on chromosomes 1 (2 QTLs), 2 and 3; three QTLs for panicle number per plant on chromosomes 1 (2 QTLs) and 3; four QTLs for plant height on chromosomes 2, 4, 5 and 6; one QTL for spikelet density on chromosome 5; four QTLs for spikelet fertility percentage (SFP) on chromosomes 2, 3 and 5 (2 QTLs); two QTLs for grain length on chromosomes 1 and 8; three QTLs for grain width on chromosomes1, 3 and 8; three QTLs for 1000-grain weight (TGW) on chromosomes 1, 4 and 8 and six QTLs for yield per plant (YPP) on chromosomes 2 (3 QTLs), 4, 6 and 8. Most of the QTLs were detected on chromosome 2, so further studies on chromosome 2 could help unlock some new chapters of QTL for this cross of rice variety. Identified QTLs elucidating high phenotypic variance can be used for marker-assisted selection (MAS) breeding. Further, the exploitation of information regarding molecular markers tightly linked to QTLs governing these traits will facilitate future crop improvement strategies in rice.     

Discovering Candidate Chromosomal Regions Linked to Kernel Size-Related Traits via QTL Mapping and Bulked Sample Analysis in Maize

Kernel size-related traits, including kernel length, kernel width, and kernel thickness, are critical components in determining yield and kernel quality in maize (Zea mays L.). Dissecting the phenotypic characteristics of these traits, and discovering the candidate chromosomal regions for these traits, are of potential importance for maize yield and quality improvement. In this study, a total of 139 F2:3 family lines derived from EHel and B73, a distinct line with extremely low ear height (EHel), was used for phenotyping and QTL mapping of three kernel size-related traits, including 10-kernel length (KL), 10-kernel width (KWid), and 10-kernel thickness (KT). The results showed that only one QTL for KWid, i.e., qKWid9 on Chr9, with a phenotypic variation explained (PVE) of 13.4% was detected between SNPs of AX-86298371 and AX-86298372, while no QTLs were detected for KL and KT across all 10 chromosomes. Four bulked groups of family lines, i.e., Groups I to IV, were constructed with F2:3 family lines according to the phenotypic comparisons of KWid between EHel and B73. Among these four groups, Group I possessed a significantly lower KWid than EHel (P = 0.0455), Group II was similar to EHel (P = 0.34), while both Group III and Group IV were statistically higher than EHel (P < 0.05). Besides, except Group IV exhibited a similar KWid to B73 (P = 0.11), KWid of Groups I to III were statistically lower than B73 (P < 0.00). By comparing the bulked genotypes of the four groups to EHel and B73, a stable chromosomal region on Chr9 between SNPs of AX-86298372 to AX-86263154, entirely covered by qKWid9, was identified to link KWid with the positive allele of increasing phenotypic effect to KWid from B73, similar to that of qKWid9. A large amount of enzyme activity and macromolecule binding-related genes were annotated within this chromosomal region, suggesting qKWid9 as a potential QTL for KWid in maize.     

Quantitative trait loci and candidate genes underlying genotype by environment interaction in the response of Arabidopsis thaliana to drought

Drought stress was imposed on two sets of Arabidopsis thaliana genotypes grown in sand under short‐day conditions and analysed for several shoot and root growth traits. The response to drought was assessed for quantitative trait locus (QTL) mapping in a genetically diverse set of Arabidopsis accessions using genome‐wide association (GWA) mapping, and conventional linkage analysis of a recombinant inbred line (RIL) population. Results showed significant genotype by environment interaction (G×E) for all traits in response to different watering regimes. For the RIL population, the observed G×E was reflected in 17 QTL by environment interactions (Q×E), while 17 additional QTLs were mapped not showing Q×E. GWA mapping identified 58 single nucleotide polymorphism (SNPs) associated with loci displaying Q×E and an additional 16 SNPs associated with loci not showing Q×E. Many candidate genes potentially underlying these loci were suggested. The genes for RPS3C and YLS7 were found to contain conserved amino acid differences when comparing Arabidopsis accessions with strongly contrasting drought response phenotypes, further supporting their candidacy. One of these candidate genes co‐located with a QTL mapped in the RIL population.     

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait

Understanding the genetic basis of traits involved in adaptation is a major challenge in evolutionary biology but remains poorly understood. Here, we use genome-wide association mapping using a custom 50 k single nucleotide polymorphism (SNP) array in a natural population of collared flycatchers to examine the genetic basis of clutch size, an important life-history trait in many animal species. We found evidence for an association on chromosome 18 where one SNP significant at the genome-wide level explained 3.9% of the phenotypic variance. We also detected two suggestive quantitative trait loci (QTLs) on chromosomes 9 and 26. Fitness differences among genotypes were generally weak and not significant, although there was some indication of a sex-by-genotype interaction for lifetime reproductive success at the suggestive QTL on chromosome 26. This implies that sexual antagonism may play a role in maintaining genetic variation at this QTL. Our findings provide candidate regions for a classic avian life-history trait that will be useful for future studies examining the molecular and cellular function of, as well as evolutionary mechanisms operating at, these loci.     

甜瓜果实糖含量相关性状QTL分析

以高糖栽培亲本自交系‘0246’为母本,低糖野生亲本自交系‘Y101’为父本,通过杂交得到了含135个单株的甜瓜远缘F2群体,分别测定甜瓜果实果糖、葡萄糖和蔗糖含量,将三者之和作为总糖含量,进行遗传连锁图谱构建及QTL分析。结果表明:(1)构建的甜瓜果实遗传图谱包含14个连锁群,覆盖基因组长度726.30cM,标记间平均距离为12.74cM。(2)检测到与总糖含量和果糖含量相关的QTL位点各1个,分别命名为Ts3.1和Fru4.1,贡献率分别为14.89%和13.02%,分布于第3、4连锁群,LOD值分别为3.60和3.10。2个QTL位点均为正向加性遗传,分别对增加总糖和果糖含量表现为增效累加效应。研究结果为开展甜瓜糖含量相关基因精细定位和克隆研究奠定了基础。     

Efficiently Tracking Selection in a Multiparental Population: The Case of Earliness in Wheat

Multiparental populations are innovative tools for fine mapping large numbers of loci. Here we explored the application of a wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population for QTL mapping. This population was created by 12 generations of free recombination among 60 founder lines, following modification of the mating system from strict selfing to strict outcrossing using the ms1b nuclear male sterility gene. Available parents and a subset of 380 SSD lines of the resulting MAGIC population were phenotyped for earliness and genotyped with the 9K i-Select SNP array and additional markers in candidate genes controlling heading date. We demonstrated that 12 generations of strict outcrossing rapidly and drastically reduced linkage disequilibrium to very low levels even at short map distances and also greatly reduced the population structure exhibited among the parents. We developed a Bayesian method, based on allelic frequency, to estimate the contribution of each parent in the evolved population. To detect loci under selection and estimate selective pressure, we also developed a new method comparing shifts in allelic frequency between the initial and the evolved populations due to both selection and genetic drift with expectations under drift only. This evolutionary approach allowed us to identify 26 genomic areas under selection. Using association tests between flowering time and polymorphisms, 6 of these genomic areas appeared to carry flowering time QTL, 1 of which corresponds to Ppd-D1, a major gene involved in the photoperiod sensitivity. Frequency shifts at 4 of 6 areas were consistent with earlier flowering of the evolved population relative to the initial population. The use of this new outcrossing wheat population, mixing numerous initial parental lines through multiple generations of panmixia, is discussed in terms of power to detect genes under selection and association mapping. Furthermore we provide new statistical methods for use in future analyses of multiparental populations.     

Allelic Variation,Aneuploidy, and Nongenetic Mechanisms Suppress a Monogenic Trait in Yeast

Clinically relevant features of monogenic diseases, including severity of symptoms and age of onset, can vary widely in response to environmental differences as well as to the presence of genetic modifiers affecting the trait’s penetrance and expressivity. While a better understanding of modifier loci could lead to treatments for Mendelian diseases, the rarity of individuals harboring both a disease-causing allele and a modifying genotype hinders their study in human populations. We examined the genetic architecture of monogenic trait modifiers using a well-characterized yeast model of the human Mendelian disease classic galactosemia. Yeast strains with loss-of-function mutations in the yeast ortholog (GAL7) of the human disease gene (GALT) fail to grow in the presence of even small amounts of galactose due to accumulation of the same toxic intermediates that poison human cells. To isolate and individually genotype large numbers of the very rare (∼0.1%) galactose-tolerant recombinant progeny from a cross between two gal7Δ parents, we developed a new method, called “FACS-QTL.” FACS-QTL improves upon the currently used approaches of bulk segregant analysis and extreme QTL mapping by requiring less genome engineering and strain manipulation as well as maintaining individual genotype information. Our results identified multiple distinct solutions by which the monogenic trait could be suppressed, including genetic and nongenetic mechanisms as well as frequent aneuploidy. Taken together, our results imply that the modifiers of monogenic traits are likely to be genetically complex and heterogeneous.     

Genome-wide SNP identification for the construction of a high-resolution genetic map of Japanese flounder (Paralichthys olivaceus): applications to QTL mapping of Vibrio anguillarum disease resistance and comparative genomic analysis

High-resolution genetic maps are essential for fine mapping of complex traits, genome assembly, and comparative genomic analysis. Single-nucleotide polymorphisms (SNPs) are the primary molecular markers used for genetic map construction. In this study, we identified 13,362 SNPs evenly distributed across the Japanese flounder (Paralichthys olivaceus) genome. Of these SNPs, 12,712 high-confidence SNPs were subjected to high-throughput genotyping and assigned to 24 consensus linkage groups (LGs). The total length of the genetic linkage map was 3,497.29 cM with an average distance of 0.47 cM between loci, thereby representing the densest genetic map currently reported for Japanese flounder. Nine positive quantitative trait loci (QTLs) forming two main clusters for Vibrio anguillarum disease resistance were detected. All QTLs could explain 5.1–8.38% of the total phenotypic variation. Synteny analysis of the QTL regions on the genome assembly revealed 12 immune-related genes, among them 4 genes strongly associated with V. anguillarum disease resistance. In addition, 246 genome assembly scaffolds with an average size of 21.79 Mb were anchored onto the LGs; these scaffolds, comprising 522.99 Mb, represented 95.78% of assembled genomic sequences. The mapped assembly scaffolds in Japanese flounder were used for genome synteny analyses against zebrafish (Danio rerio) and medaka (Oryzias latipes). Flounder and medaka were found to possess almost one-to-one synteny, whereas flounder and zebrafish exhibited a multi-syntenic correspondence. The newly developed high-resolution genetic map, which will facilitate QTL mapping, scaffold assembly, and genome synteny analysis of Japanese flounder, marks a milestone in the ongoing genome project for this species.