Related Quantitative Trait Loci Research Articles

Genotyping by sequencing for the construction of oil palm (Elaeis guineensis Jacq.) genetic linkage map and mapping of yield related quantitative trait loci.

Oil palm (Elaeis guineensis Jacq.) is one of the major oil-producing crops. Improving the quality and increasing the production yield of oil palm have been the primary focuses of both conventional and modern breeding approaches. However, the conventional breeding approach for oil palm is very challenging due to its longevity, which results in a long breeding cycle. Thus, the establishment of marker assisted selection (MAS) for oil palm breeding programs would speed up the breeding pipeline by generating new oil palm varieties that possess high commercial traits. With the decreasing cost of sequencing, Genotyping-by-sequencing (GBS) is currently feasible to many researchers and it provides a platform to accelerate the discovery of single nucleotide polymorphism (SNP) as well as insertion and deletion (InDel) markers for the construction of a genetic linkage map. A genetic linkage map facilitates the identification of significant DNA regions associated with the trait of interest via quantitative trait loci (QTL) analysis. A mapping population of 112 F1 individuals from a cross of Deli dura and Serdang pisifera was used in this study. GBS libraries were constructed using the double digestion method with HindIII and TaqI enzymes. Reduced representation libraries (RRL) of 112 F1 progeny and their parents were sequenced and the reads were mapped against the E. guineensis reference genome. To construct the oil palm genetic linkage map, informative SNP and InDel markers were used to discover significant DNA regions associated with the traits of interest. The nine traits of interest in this study were fresh fruit bunch (FFB) yield, oil yield (OY), oil to bunch ratio (O/B), oil to dry mesocarp ratio (O/DM) ratio, oil to wet mesocarp ratio (O/WM), mesocarp to fruit ratio (M/F), kernel to fruit ratio (K/F), shell to fruit ratio (S/F), and fruit to bunch ratio (F/B). A total of 2.5 million SNP and 153,547 InDel markers were identified. However, only a subset of 5,278 markers comprising of 4,838 SNPs and 440 InDels were informative for the construction of a genetic linkage map. Sixteen linkage groups were produced, spanning 2,737.6 cM for the maternal map and 4,571.6 cM for the paternal map, with average marker densities of one marker per 2.9 cM and one per 2.0 cM respectively, were produced. A QTL analysis was performed on nine traits; however, only QTL regions linked to M/F, K/F and S/F were declared to be significant. Of those QTLs were detected: two for M/F, four for K/F and one for S/F. These QTLs explained 18.1-25.6% of the phenotypic variance and were located near putative genes, such as casein kinase II and the zinc finger CCCH domain, which are involved in seed germination and growth. The identified QTL regions for M/F, K/F and S/F from this study could be applied in an oil palm breeding program and used to screen palms with desired traits via marker assisted selection (MAS).

The selected genes NR6A1, RSAD2-CMPK2, and COL3A1 contribute to body size variation in Meishan pigs through different patterns.

The high-fertility Meishan pig is currently categorized into medium sized (MMS) and small sized (SMS) based on body size. To identify causal genes responsible for the variation in body size within the two categories, we sequenced individuals representing the entire consanguinity of the existing Meishan pig. This enabled us to conduct genome selective signal analysis. Our findings revealed the genomes of MMS and SMS are stratified, with selective sweep regions formed by differential genomic intervals between the two categories enriched in multiple pig body size related quantitative trait loci (QTLs). Furthermore, the missense mutation c.575T > C of candidate causal gene NR6A1, accounting for the variation in lumbar vertebrae number in pigs, was positively selected in MMS only, leading to an increase in body length of MMS at 6 months of age. To precisely identify causal genes accounting for body size variation through multi-omics, we collected femoral cartilage and liver transcription data from MMS and SMS respectively, and re-sequencing data from pig breeds exhibiting varying body sizes. We found that two selected regions where the RSAD2-CMPK2 and COL3A1 genes are located, respectively, showed different haplotypes in pig breeds of varying body size, and was associated with body or carcass length in hybridized Suhuai pig. Additionally, the above three hub genes, were significantly greater expressed in SMS femoral cartilage and liver tissues compared to MMS. These three genes could strengthen the pathways related to bone resorption and metabolism in SMS, potentially hindering bone and skeletal development and resulting in a smaller body size in SMS. These findings provide valuable insights into the genetic mechanism of body size variation in Meishan pig population.

Role of Wheat Phosphorus Starvation Tolerance 1 Genes in Phosphorus Acquisition and Root Architecture.

The wheat plant requires elevated phosphorus levels for its normal growth and yield, but continuously depleting non-renewable phosphorus reserves in the soil is one of the biggest challenges in agricultural production worldwide. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been reported to play a key role in efficient P uptake, deeper rooting, and high yield in rice. However, the function of the PSTOL1 gene in wheat is still unclear. In this study, a total of 22 PSTOL1 orthologs were identified in the wheat genome, and found that wheat PSTOL1 orthologs are unevenly distributed on chromosomes, and these genes were under strong purifying selection. Under different phosphorus regimes, wheat PSTOL1 genes showed differential expression patterns in different tissues. These results strengthen the classification of Pakistan-13 as a P-efficient cultivar and Shafaq-06 as a P-inefficient cultivar. Phenotypic characterization demonstrated that Pakistan-13 wheat cultivar has significantly increased P uptake, root length, root volume, and root surface area compared to Shafaq-06. Some wheat PSTOL1 orthologs are co-localized with phosphorus starvation’s related quantitative trait loci (QTLs), suggesting their potential role in phosphorus use efficiency. Altogether, these results highlight the role of the wheat PSTOL1 genes in wheat P uptake, root architecture, and efficient plant growth. This comprehensive study will be helpful for devising sustainable strategies for wheat crop production and adaptation to phosphorus insufficiency.

Quantitative trait locus mapping of fruit aroma compounds in cucumber (Cucumber sativus L.) based on a recombinant inbred line population.

The fresh and unique flavor of cucumber fruits, mainly composed of aldehydes and alcohols, is one of its most important fruit qualities. However, little is known about the genetic basis of aroma compounds in cucumber fruit and the related quantitative trait loci (QTLs). In this study, genomic screening of QTLs underlying aroma compounds was performed based on the genetic linkage map constructed using 1301 single-nucleotide polymorphism (SNP) markers from genotyping-by-sequencing of a recombinant inbred line (RIL) population developed from Q16 × Q24. Significant genetic variations of aroma compounds in the RIL population were observed, and a total of 28 QTLs were screened. A major QTL (qol8-2.1) related to (E,Z)-2,6-nonadien-1-ol was detected with a markedly high LOD score (10.97 in 2020 and 3.56 in 2019) between mk190 and mk204 on chromosome 2. Genome scans identified a cluster of nine lipoxygenase genes in this region. A significant positive correlation was detected between CsaV3_2G005360 (CsLOX08) and (E,Z)-2,6-nonadien-1-ol, and five amino acid variations were detected between the CsLOX08 protein sequences of the two parental lines. Based on the genome variation of CsLOX08, we developed an InDel marker. Genotyping of InDel markers was consistent with the content of (E,Z)-2,6-nonadien-1-ol in RILs, which were also verified in nine cucumber inbred lines. The results will give breeders guidance for obtaining better flavor in cucumber.

Role of molecular markers in improving abiotic stress tolerance in agricultural crops

Molecular markers are one of the expandable inventions in agricultural science. After decades of their introduction, these still are an integral part of crop genotyping and crop improvement. The present scenario offers to choose from different molecular marker types based on their principle, methodologies and extent of applications. Several markers have been used to identify and map abiotic stress related genes and quantitative trait loci (QTL) onto the chromosomes of different crops. The genetic mapping of these identified genetic elements by using different markers provides the scope of selective breeding in the agricultural crops to tackle abiotic stresses. Moreover, recent progress achieved in genetics, molecular breeding and genomic selection has facilitated a comprehensive understanding of the molecular markers and unlocked new insights into marker-assisted breeding. The advent of new technologies like association mapping (AM) and genome-wide association studies has unveiled the highthroughput application of molecular markers. In this review, a focused representation of the use of different molecular markers in the identification of tolerant crop genotypes and associated genes/QTLs against major abiotic stresses, including salinity, drought and temperature has been provided. Additionally, the application of molecular markers in AM and AM-based breeding of some important agricultural crops has been discussed.

Mapping QTL for leaf pigment content at dynamic development stage and analyzing Meta-QTL in rice

Leaf pigment content is a complicated quantitative trait which results from the cooperation of multiple related genes or quantitative trait loci (QTL) in rice. So far, more than 600 QTL for leaf pigment content has been reported. However, most QTL positions could not be directly compared with each other. In this study, our goal was to analyze consistent QTL regions affecting leaf pigment content by applying a genome wide QTL meta-analysis approach. 20 QTL related to leaf pigment content were detected at 5 different growth periods in 134 recombinant inbred lines (RILs) from a typical Indica-Japonica cross derived from PA64s and 9311 (two parents of super hybrid rice Liangyoupei 9). There was a candidate gene GLTP in the region of 3 QTL (qFS_Chla4, qFS_Chla+b4, and qFS_Car4), which related to component of chloroplast thylakoid membranes. After sequencing and qRT-PCR analysis, the gene showed significant difference in parents of the RILs. Meta-analysis was performed on 618 QTL collected from 38 previous studies. Consequently, a total of 64 MQTL (Meta-QTL) were obtained, of which 58.95% confidence intervals (CI) were smaller than the average Cl of the original QTL. In addition, 64 MQTL covered 6 of 20 QTL detected. Among them, four main QTL were included in 3 MQTL, and phenotypic variation of 21 MQTL was greater than 20%. The traits with higher number of QTL had higher number of MQTL, and candidate genes in overlapping MQTL include multiple effects. 7 candidate genes related to leaf pigment content were found in 4 MQTL spanning physical intervals < 0.5 Mb. These findings are not only anticipated to help molecular marker-assisted selection and pyramiding, but also contribute to determine candidate genes that regulate pigment content.

Identification and characterisation of cold stress-related proteins in Oryza rufipogon at the seedling stage using label-free quantitative proteomic analysis.

In this study, label-free quantitative proteomics were used to study cold stress-related proteins in Dongxiang wild rice (Oryza rufipogon Griff., DWR) and cold sensitive cultivated rice 'Xieqingzao B'(Oryza sativa L. ssp. indica cv., XB). The results demonstrated the presence of 101 and 216 differentially expressed proteins (DEPs) were detected in DWR and XB, respectively, after cold stress. Bioinformatics analysis showed that DWR and XB differed significantly in their ability to scavenge reactive oxygen species (ROS) and regulate energy metabolism. Of the 101 DEPs of DWR, 46 DEPs related to differential expressed genes were also detected by transcriptome analysis. And 13 out of 101 DEPs were located in previous cold related quantitative trait loci (QTL). Quantitative real-time PCR analysis indicated that protein expression and transcription patterns were not similar in XB and DWR. Protein-protein interaction (PPI) network was constituted using the DEPs of DWR and XB, and the following three centre proteins were identified: Q8H3I3, Q9LDN2, and Q2QXR8. Next, we selected a centre protein and two of the 37 DEPs with high levels of differential expression (fold change ≥ 2) were used for cloning and prokaryotic expression. We found that Q5Z9Q8 could significantly improve the cold tolerance of Escherichia coli.

Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids.

RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively, were generated and aligned against the Nipponbare reference genome. Transcriptome profiling of Ajay revealed 2814 and 4819 differentially expressed genes (DEGs) at the PI and GF stages, respectively, as compared to its parents. In the case of Rajalaxmi, 660 and 5264 DEGs were identified at PI and GF stages, respectively. Functionally relevant DEGs were selected for validation through qRT-PCR, which were found to be co-related with the expression patterns to RNA-seq. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated significant DEGs enriched for energy metabolism pathways, such as photosynthesis, oxidative phosphorylation, and carbon fixation, at the PI stage, while carbohydrate metabolism-related pathways, such as glycolysis and starch and sucrose metabolism, were significantly involved at the GF stage. Many genes involved in energy metabolism exhibited upregulation at the PI stage, whereas the genes involved in carbohydrate biosynthesis had higher expression at the GF stage. The majority of the DEGs were successfully mapped to know yield related rice quantitative trait loci (QTLs). A set of important transcription factors (TFs) was found to be encoded by the identified DEGs. Our results indicated that a complex interplay of several genes in different pathways contributes to higher yield and vigor in rice hybrids.

High resolution genetic mapping and identification of a candidate gene(s) for the purple sheath color and plant height in an interspecific F2 population derived from Oryza nivara Sharma &amp; Shastry × Oryza sativa L. cross

Wild relatives of rice (Oryza sativa L.) represent enormous genetic diversity for many traits. Many domestication related traits found only in wild species that are lost from cultivated species during domestication. In this study, we report high-resolution mapping of two domestications related quantitative trait locus (QTL) controlling purple sheath color and plant height using high-density SNP based linkage map in an interspecific F2 population derived from a cross between O. nivara Sharma & Shastry and O. sativa. The segregation ratio of purple sheath color fit into 3:1 indicated that the presence of a dominant gene. The segregation of plant height trait exhibited a normal distribution in F2 and F2:3 generations. QTL analysis showed the identification of two QTLs controlling purple sheath color (designated as qPsh6.1 and qPsh6.2) on chromosome 6 explaining 27.12% and 14% phenotypic variance, respectively. The only plant height QTL (tentatively designated as qPh1.9) was mapped on chromosome 1 contributing 18.3% phenotypic variance. The qPsh6.1 covers 25.17 Kb region flanked by AX-95928721 and AX-95954573 containing five open reading frames (ORFs) while qPsh6.2 spanned in 118.2 Kb region containing 19 ORFs flanked by markers AX-95956260 and AX-95928295. The qPh1.9 gene controlling plant height was mapped between two SNP markers, AX-95944819 and AX-95964796 co-segregated with the locus LOC_Os01g66690 encoding for ZIP4/SPO22 protein. The detailed genetic study of the location of these genes will be useful for the map-based cloning.

Current understanding of genetic and molecular basis of cold tolerance in rice

Rice (Oryza sativa L.) is one of the most important crops worldwide, but its growth and production can be severely affected by climate change. As a tropical species, rice is in general vulnerable to the adverse effects of low temperature. To cope with or adapt to cold stress condition, rice has evolved elaborate regulatory mechanisms under both natural and artificial selection. Over the past few decades, intensive research efforts have been focused on abiotic stress biology in rice with genetic, genomic, and molecular strategies, disclosing a series of potential genetic determinants and mechanisms controlling cold stress tolerance. Here, we review cold tolerance (CT)-related quantitative trait loci (QTLs) identified by linkage and association mapping, together with key genes involved in cold sensing, signaling, and response. More importantly, recent studies have shown that CT-related QTLs/genes can be employed in genomic breeding aiming at developing cold-tolerant rice. Overall, the recent research progresses in understanding the complex genetic and molecular mechanisms of CT provide a substantial basis for CT improvement in rice.

Identification of quantitative trait loci (QTLs) linked to Apple chlorotic leaf spot virus (ACLSV) resistance in apricot

Apple chlorotic leaf spot virus (ACLSV), also known as apricot pseudo pox, “viruela” (in Spain) and “butteratura” (in Italy), has had a significant impact on the production of Prunus species, including apricot (P. armeniaca L.). Two apricot cultivars have recently been described as resistant to this virus: the traditional Spanish cultivar ‘Mauricio’ and the French cultivar ‘Bergeron’. However, as far as we know, no work on the genetic control of the resistance to ACLSV has been published in any Prunus species. In this study, the transmission of resistance to ACLSV and the related quantitative trait loci (QTLs) were analysed for 3 years in an F1 apricot progeny of 130 descendants derived from the cross ‘Bergeron’ (resistant to ACLSV) × ‘Currot’ (susceptible). The apricot descendants evaluated were classified as susceptible or resistant depending on the presence or absence of ACLSV evaluated through ELISA and RT-PCR. A non-parametric mapping method based on the Kruskal–Wallis (KW) test was used to score and identify linked QTLs. The ‘Bergeron’ cultivar showed a high capacity to transmit resistance to ACLSV, generating around 57% of the resistant descendants. Additionally, the results indicated an oligogenic control of ACLSV resistance in apricot, with significant QTLs in alternative years in linkage groups (LGs) 5 and 7 and in all years in LG2 and LG4.

Detection of circular RNA expression and related quantitative trait loci in the human dorsolateral prefrontal cortex

BackgroundCircular RNAs (circRNAs) are implicated in various biological processes. As a layer of the gene regulatory network, circRNA expression is also an intermediate phenotype bridging genetic variation and phenotypic changes. Thus, analyzing circRNA expression variation will shed light on molecular fundamentals of complex traits and diseases.ResultsWe systematically characterize 10,559 high-quality circRNAs in 589 human dorsolateral prefrontal cortex samples. We identify biological and technical factors contributing to expression heterogeneity associated with the expression levels of many circRNAs, including the well-known circRNA CDR1as. Combining the expression levels of circRNAs with genetic cis-acting SNPs, we detect 196,255 circRNA quantitative trait loci (circQTLs). By characterizing circQTL SNPs, we find that partial circQTL SNPs might influence circRNA formation by altering the canonical splicing site or the reverse complementary sequence match. Additionally, we find that a subset of these circQTL SNPs is highly linked to genome-wide association study signals of complex diseases, especially schizophrenia, inflammatory bowel disease, and type II diabetes mellitus.ConclusionsOur results reveal technical, biological, and genetic factors affecting circRNA expression variation among individuals, which lead to further understanding of circRNA regulation and thus of the genetic architecture of complex traits or diseases.

Linkage-based genome assembly improvement of oil palm (Elaeis guineensis)

Meiotic crossovers in outbred species, such as oil palm (Elaeis guineensis Jacq., 2n = 32) contribute to allelic re-assortment in the genome. Such genetic variation is usually exploited in breeding to combine positive alleles for trait superiority. A good quality reference genome is essential for identifying the genetic factors underlying traits of interest through linkage or association studies. At the moment, an AVROS pisifera genome is publicly available for oil palm. Distribution and frequency of crossovers throughout chromosomes in different origins of oil palm are still unclear. Hence, an ultrahigh-density genomic linkage map of a commercial Deli dura x AVROS pisifera family was constructed using the OP200K SNP array, to evaluate the genetic alignment with the genome assembly. A total of 27,890 linked SNP markers generated a total map length of 1,151.7 cM and an average mapping interval of 0.04 cM. Nineteen linkage groups represented 16 pseudo-chromosomes of oil palm, with 61.7% of the mapped SNPs present in the published genome. Meanwhile, the physical map was also successfully extended from 658 Mb to 969 Mb by assigning unplaced scaffolds to the pseudo-chromosomes. A genic linkage map with major representation of sugar and lipid biosynthesis pathways was subsequently built for future studies on oil related quantitative trait loci (QTL). This study improves the current physical genome of the commercial oil palm, and provides important insights into its recombination landscape, eventually unlocking the full potential genome sequence-enabled biology for oil palm.

Updating the Genome of the Elite Rice Variety Kongyu131 to Expand Its Ecological Adaptation Region.

As an elite rice variety cultivated in the third accumulative temperature belt in Heilongjiang province, China, Kongyu131 has many excellent traits, such as high quality, high stability, early maturation and cold resistance. However, as with other crop varieties, Kongyu131 has regional restrictions, exhibiting decreased yields when grown at low latitudes. To address these problems, two populations were constructed from cross between japonica and indica varieties. QTL analyses were performed with these two populations to detect regional adaptation related quantitative trait locus. Results in a BC1F6 backcross inbred line population with 168 lines derived from cross between Kongyu131 and GKMP showed a large pleiotropic QTL near 9 Mb on chromosome 7, which significantly delayed the HD of Kongyu131 and increased the plant height (PH), length of main panicle (LMP), number of primary branches (NPB) and grain number of main panicles (GNP). We also found a similar QTL in the population BC3F2 derived from Kongyu131 and GKLPL. Based on the QTL, we developed a gene module named mRA7 with 5 single-nucleotide polymorphism (SNP) markers around the QTL. Through a foreground and background selection based on 197 SNP markers evenly distributed over the 12 chromosomes, we obtained a new plant (a single point substitution line, SPSL) with a new Kongyu131 genome, carrying only a small chromosomal fragment less than 800 kb from GKLPL. The background recovery ratio of the SPSL was 99.8%. Compared with Kongyu131, the SPSL exhibited a significant HD delay of approximately 31 days and increased PH, LMP and GNP values when planted in Heilongjiang province. When cultivated in Guangdong province, HD of SPSL showed only 16 days delay, and less increase in PH, LMP and GNP than in Heilongjiang province. Phenotypic evaluation showed that the SPSL could be moved to south by more than 3 latitude units and cultivated in low-latitude regions. This study exemplifies the feasibility of expanding the regions of cultivation of elite rice varieties via similar methods.

From in planta Function to Vitamin-Rich Food Crops: The ACE of Biofortification.

Humans are highly dependent on plants to reach their dietary requirements, as plant products contribute both to energy and essential nutrients. For many decades, plant breeders have been able to gradually increase yields of several staple crops, thereby alleviating nutritional needs with varying degrees of success. However, many staple crops such as rice, wheat and corn, although delivering sufficient calories, fail to satisfy micronutrient demands, causing the so called ‘hidden hunger.’ Biofortification, the process of augmenting nutritional quality of food through the use of agricultural methodologies, is a pivotal asset in the fight against micronutrient malnutrition, mainly due to vitamin and mineral deficiencies. Several technical advances have led to recent breakthroughs. Nutritional genomics has come to fruition based on marker-assisted breeding enabling rapid identification of micronutrient related quantitative trait loci (QTL) in the germplasm of interest. As a complement to these breeding techniques, metabolic engineering approaches, relying on a continuously growing fundamental knowledge of plant metabolism, are able to overcome some of the inevitable pitfalls of breeding. Alteration of micronutrient levels does also require fundamental knowledge about their role and influence on plant growth and development. This review focuses on our knowledge about provitamin A (beta-carotene), vitamin C (ascorbate) and the vitamin E group (tocochromanols). We begin by providing an overview of the functions of these vitamins in planta, followed by highlighting some of the achievements in the nutritional enhancement of food crops via conventional breeding and genetic modification, concluding with an evaluation of the need for such biofortification interventions. The review further elaborates on the vast potential of creating nutritionally enhanced crops through multi-pathway engineering and the synergistic potential of conventional breeding in combination with genetic engineering, including the impact of novel genome editing technologies.

QTL for Sensitivity of Seedling Height to Exogenous GA3 and Their Effects on Adult Plant Height in Common Wheat

Plants with deficiency in Gibberellins (GAs) biosynthesis pathway are sensitive to exogenous GA3, while those with deficiency in GAs signaling pathway are insensitive to exogenous GA3. Thus, exogenous GA3 test is often used to verify whether the reduced height (Rht) gene is involved in GAs biosynthesis or signaling pathway. In the present study, we identified the genetic factors responsive to exogenous GA3 at the seedling stage of common wheat and analyzed the response of the plant height related quantitative trait loci (QTL) to GA3 to understand the GAs pathways the Rht participated in. Recombinant inbred lines derived from a cross between KN9204 and J411 with different response to exogenous GA3 were used to screen QTL for the sensitivity of coleoptile length (SCL) and the sensitivity of seedling plant height (SSPH) to exogenous GA3. Two additive QTL and two pairs of epistatic QTL for SCL were identified, meanwhile, two additive QTL and three pairs of epistatic QTL for SSPH were detected. For the adult plant height (PH) investigated in two environments, six additive QTL were identified. Three QTL qScl-4B, qSsph-4B and qPh-4B were mapped in one cluster near the functional marker Rht-B1b. When PH were conditional on SSPH, the absolute additive effect value of qPh-4B and qPh-6B were reduced, suggesting that the Rhts in both two QTL were insensitive to exogenous GA3, while the additive effect values of qPh-2B, qPh-3A, qPh-3D and qPh-5A were not significantly changed, indicating that the Rhts in these QTL were sensitive to exogenous GA3, or they were not expressed at the seedling stage.

Comparative alternative splicing analysis of two contrasting rice cultivars under drought stress and association of differential splicing genes with drought response QTLs

Alternative splicing (AS) of precursor mRNA is often regulated by different developmental stages, environments, and genotypes. Little is known about how AS is regulated between different rice cultivars with distinctive response to certain abiotic stress. This study aimed to elucidate the AS patterns in contrasting rice (Oryza sativa L.) cultivars and examine its role during rice adaptation to drought environment. By comparing AS patterns between IRAT109 and ZS97 rice cultivars under drought stress, drought tolerant and susceptible respectively, 8034 shared, 11,086 ZS97-specific, and 12,057 IRAT109-specific AS events were observed where intron retention is the predominant AS pattern. Gene ontology (GO) as well as Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enrichment analyses suggested that the spliceosome and DNA repair represented the most significant functional categories among the genes with genotype-specific AS patterns. Other categories include basal transcription factors, environmental information, adaptation related pathways, oxidative phosphorylation, etc. Through integrating the drought-response related quantitative trait locus (QTLs) from 2006 to 2016 manually and mapping spliceosome and DNA repair genes with different AS patterns on chromosomes, we identified 14 out of 31 genes involved in splicesome and 4 out of 14 genes in DNA repair co-localized in drought stress related QTLs. We therefore propose that during long domestication, genes responsive to drought stress evolved specific AS patterns in upland rice, and spliceosome and DNA repair genes play potential roles in rice tolerance to drought stress. Genes with diversity AS patterns and co-localized with drought QTLs will serve as important resources for genetic improvement of rice adaptation to drought stress.

Mapping quantitative trait loci for heat tolerance at the booting stage using chromosomal segment substitution lines in rice.

High temperature stress is a major obstacle in rice productivity. Considerable progress has been made on studying heat tolerance (HT) at different stages. However, the genetic basis of HT at the booting stage is poorly understood. In this study, we analyzed the morphological features of a heat-sensitive japonica cultivar Sasanishiki under natural high temperature stress at the booting stage. The anthers became smaller and the number, and fertility, of pollen grains were decreased significantly. As a result, there was a dramatic reduction in spikelet fertility. In contrast, the indica cultivar Habataki showed high HT and normal spikelet fertility under high temperature stress. Additonally, a set of chromosome segment substitution lines, derived from Sasanishiki and Habataki, were evaluated for HT related quantitative trait loci (QTLs) across two environments in the natural field. A total of 12 QTLs associated with HT were detected, of which, 5 were identified in two environments, and 7 in one environment. Furthermore, one of the major-effect QTLs (qHTB3-3) detected on the long arm of chromosome 3, was confirmed using overlapping substituted lines. qHTB3-3 was finally mapped between the two markers RM3525 and 3-M95, approximately 2.8Mb apart. These findings and further gene cloning of qHTB3-3 will help us better understand the molecular control of HT in rice, and may contribute to the development of high HT rice varieties.

Genome-wide mapping of large deletions and their population-genetic properties in dairy cattle.

Large genomic deletions are potential candidate for loss-of-function, which could be lethal as homozygote. Analysing whole genome data of 175 cattle, we report 8,480 large deletions (199 bp–773 KB) with an overall false discovery rate of 8.8%; 82% of which are novel compared with deletions in the dbVar database. Breakpoint sequence analyses revealed that majority (24 of 29 tested) of the deletions contain microhomology/homology at breakpoint, and therefore, most likely generated by microhomology-mediated end joining. We observed higher differentiation among breeds for deletions in some genic-regions, such as ABCA12, TTC1, VWA3B, TSHR, DST/BPAG1, and CD1D. The genes overlapping deletions are on average evolutionarily less conserved compared with known mouse lethal genes (P-value = 2.3 × 10−6). We report 167 natural gene knockouts in cattle that are apparently nonessential as live homozygote individuals are observed. These genes are functionally enriched for immunoglobulin domains, olfactory receptors, and MHC classes (FDR = 2.06 × 10−22, 2.06 × 10−22, 7.01 × 10−6, respectively). We also demonstrate that deletions are enriched for health and fertility related quantitative trait loci (2-and 1.5-fold enrichment, Fisher’s P-value = 8.91 × 10−10 and 7.4 × 10−11, respectively). Finally, we identified and confirmed the breakpoint of a ∼525 KB deletion on Chr23:12,291,761-12,817,087 (overlapping BTBD9, GLO1 and DNAH8), causing stillbirth in Nordic Red Cattle.

Estimating rice yield related traits and quantitative trait loci analysis under different nitrogen treatments using a simple tower-based field phenotyping system with modified single-lens reflex cameras

Application of field based high-throughput phenotyping (FB-HTP) methods for monitoring plant performance in real field conditions has a high potential to accelerate the breeding process. In this paper, we discuss the use of a simple tower based remote sensing platform using modified single-lens reflex cameras for phenotyping yield traits in rice under different nitrogen (N) treatments over three years. This tower based phenotyping platform has the advantages of simplicity, ease and stability in terms of introduction, maintenance and continual operation under field conditions. Out of six phenological stages of rice analyzed, the flowering stage was the most useful in the estimation of yield performance under field conditions. We found a high correlation between several vegetation indices (simple ratio (SR), normalized difference vegetation index (NDVI), transformed vegetation index (TVI), corrected transformed vegetation index (CTVI), soil-adjusted vegetation index (SAVI) and modified soil-adjusted vegetation index (MSAVI)) and multiple yield traits (panicle number, grain weight and shoot biomass) across a three trials. Among all of the indices studied, SR exhibited the best performance in regards to the estimation of grain weight (R2=0.80). Under our tower-based field phenotyping system (TBFPS), we identified quantitative trait loci (QTL) for yield related traits using a mapping population of chromosome segment substitution lines (CSSLs) and a single nucleotide polymorphism data set. Our findings suggest the TBFPS can be useful for the estimation of yield performance during early crop development. This can be a major opportunity for rice breeders whom desire high throughput phenotypic selection for yield performance traits.