Genetic Dissection of Epistatic Interactions Contributing Grain Yield Variability in Rice under Drought

Aims: The aim of the present study was to evaluate the performance of ‘high’-‘low’ yielding pyramided lines (PLs) with the same combinations of qDTYs in Samba Mahsuri, MR219 and IR64-Sub1 genetic backgrounds and understand the genetic interactions of QTL and with genetic background affecting grain yield. Background: Epistasis regulates the expression of traits governed by several major/minor genes/QTL. Multiple pyramided lines (PLs) with the same grain yield QTL (qDTYs) combinations but possessing grain yield variability under different levels of reproductive stage drought stress were identified in different rice genetic backgrounds at International Rice Research Institute (IRRI). Objectives: The objectives of the present study were to evaluate the performance pyramided lines (PLs) with drought QTL in the backgrounds of Samba Mahsuri, MR219 and IR64-Sub1 under reproductive stage drought stress (RS) and NS (non-stress) conditions ii) to understand the effect of epistatic interactions of qDTYs and with genetic background on GY under the differential level of stress iii) to identify the promising drought-tolerant lines with high yield under drought and higher background recovery in different genetic backgrounds. Results: Several digenic interactions were found in different genetic backgrounds, 13 interactions in Samba Mahsuri, 11 in MR219 and 20 in IR64-Sub1 backgrounds. Among all digenic interactions, one QTL × QTL interaction, 17 QTL × background and 26 background × background interactions resulted in GY reduction in low yielding PLs in different genetic backgrounds under LSS or LMS. Negative interaction of qDTY3.1, qDTY4.1 and qDTY9.1 with background markers and background × background interactions caused up to 15% GY reduction compared to the high yielding PLs under LMS in the Samba Mahsuri PLs. In MR219 PLs, the negative interaction of qDTY2.2, qDTY3.2, qDTY4.1 and qDTY12.1 with the background marker interval RM314-RM539, RM273-RM349 and RM445-RM346, RM473D-RM16, respectively resulted in 52% GY reduction compared to the high yielding PLs under LSS. In IR64-Sub1 PLs, qDTY6.1 interacted with background loci at RM16-RM135, RM228-RM333, RM202-RM287 and RM415-RM558A marker interval under LSS; and at RM475-RM525 marker interval under LMS, causing GY reduction to 58% compared to the high yielding PLs. Conclusion: High yielding PLs in Samba Mahsuri (IR 99734:1-33-69-1-22-6), MR219 (IR 99784-156-87-2-4-1) and IR64-Sub1 (IR 102784:2-89-632-2-1-2) backgrounds without any negative interactions were identified. The identified selected promising PLs may be used as potential drought-tolerant donors or may be released as varieties for drought-prone ecosystems in different countries. Methods: The experiments were conducted in 2015DS (dry season), 2015WS (wet season) and 2017 DS at IRRI, Los Baños, Philippines, in a transplanted lowland ecosystem under lowland severe stress (LSS), moderate lowland stress (LMS) and lowland non-stress (LNS). The experiments were laid out in alpha lattice design with two replications.

Analysis of barley mutants ert-c.1 and ert-d.7 reveals two loci with additive effect on plant architecture

Main conclusion Both mutant ert-c.1 and ert-d.7 carry T2-T3 translocations in the Ert-c gene. Principal coordinate analyses revealed the translocation types and translocation breakpoints. Mutant ert-d.7 is an Ert-cErt-d double mutant. Abstract Mutations in the Ert-c and Ert-d loci are among the most common barley mutations affecting plant architecture. The mutants have various degrees of erect and compact spikes, often accompanied with short and stiff culms. In the current study, complementation tests, linkage mapping, principal coordinate analyses and fine mapping were conducted. We conclude that the original ert-d.7 mutant does not only carry an ert-d mutation but also an ert-c mutation. Combined, mutations in Ert-c and Ert-d cause a pyramid-dense spike phenotype, whereas mutations in only Ert-c or Ert-d give a pyramid and dense phenotype, respectively. Associations between the Ert-c gene and T2-T3 translocations were detected in both mutant ert-c.1 and ert-d.7. Different genetic association patterns indicate different translocation breakpoints in these two mutants. Principal coordinate analysis based on genetic distance and screening of recombinants from all four ends of polymorphic regions was an efficient way to narrow down the region of interest in translocation-involved populations. The Ert-c gene was mapped to the marker interval of 2_0801to1_0224 on 3HL near the centromere. The results illuminate a complex connection between two single genes having additive effects on barley spike architecture and will facilitate the identification of the Ert-c and Ert-d genes.

Identification of a Locus Controlling Compound Raceme Inflorescence in Mungbean [Vigna radiata (L.) R. Wilczek]

Mungbean [Vigna radiata (L.) R. Wilczek] produces a compound raceme inflorescence that branches into secondary inflorescences, which produce flowers. This architecture results in the less-domesticated traits of asynchronous pod maturity and multiple harvest times. This study identified the genetic factors responsible for the compound raceme of mungbean, providing a unique biological opportunity to improve simultaneous flowering. Using a recombinant inbred line (RIL) population derived from VC1973A, an elite cultivar with a compound raceme type, and IT208075, a natural mutant with a simple raceme type, a single locus that determined the inflorescence type was identified based on 1:1 segregation ratio in the F8 generation, and designated Comraceme. Linkage map analysis showed Comraceme was located on chromosome 4 within a marker interval spanning 520 kb and containing 64 genes. RILs carrying heterozygous fragments around Comraceme produced compound racemes, indicating this form was dominant to the simple raceme type. Quantitative trait loci related to plant architecture and inflorescence have been identified in genomic regions of soybean syntenic to Comraceme. In IT208075, 15 genes were present as distinct variants not observed in other landrace varieties or wild mungbean. These genes included Vradi04g00002481, a development-related gene encoding a B3 transcriptional factor. The upstream region of Vradi04g00002481 differed between lines producing the simple and compound types of raceme. Expression of Vradi04g00002481 was significantly lower at the early vegetative stage and higher at the early reproductive stage, in IT208075 than in VC1973A. Vradi04g00002481 was therefore likely to determine inflorescence type in mungbean. Although further study is required to determine the functional mechanism, this finding provides valuable genetic information for understanding the architecture of the compound raceme in mungbean.

QTL mapping and candidate gene analysis of seed vigor-related traits during artificial aging in wheat (Triticum aestivum)

High vigor seeds have greater yield potential than those with low vigor; however, long-term storage leads to a decline in this trait. The objective of this study was to identify quantitative trait loci (QTLs) for seed vigor-related traits under artificial aging conditions using a high-density genetic linkage map of wheat (Triticum aestivum) and mine the related candidate genes. A doubled haploid population, derived from a cross between Hanxuan 10 × Lumai 14, was used as the experimental material. Six controlled-environment treatments were set up, i.e. the seeds were aged for 0, 24, 36, 48, 60, and 72 h at a high temperature (48 °C) and under high humidity (relative humidity 100%). Eight traits including seed germination percentage, germination energy, germination index, seedling length, root length, seedling weight, vigor index, and simple vigor index were measured. With the prolongation of artificial aging treatment, these traits showed a continuous downward trend and significant correlations were observed between most of them. A total of 49 additive QTLs for seed vigor-related traits were mapped onto 12 chromosomes (1B, 2D, 3A, 3B, 3D, 4A, 4D, 5A, 5B, 5D, 6D, and 7A); and each one accounted for 6.01–17.18% of the phenotypic variations. Twenty-five pairs of epistatic QTLs were detected on all chromosomes, except for 5D, 6A, and 7D, and each epistasis accounted for 7.35–26.06% of the phenotypic variations. Three additive QTL hot spots were found on chromosomes 5A, 5B, and 5D, respectively. 13 QTLs, QGEe5B, QGIe5B, QSLc5B, QSLd5B, QSLf5B, QRLd5B, QRLe5B, QRLf5B, QVId5B, QVIe5B, QVIf5B, QSVId5B, and QSVIe5B, were located in the marker interval AX-94643729 ~ AX-110529646 on 5B and the physical interval 707,412,449–710,959,479 bp. Genes including TRAESCS5B01G564900, TRAESCS5B01G564200, TRAESCS5B01G562600, TraesCS5B02G562700, TRAESCS5B01G561300, TRAESCS5B01G561400, and TRAESCS5B01G562100, located in this marker interval, were found to be involved in regulating the processes of carbohydrate and lipid metabolism, transcription, and cell division during the germination of aging seeds, thus they were viewed as candidate genes for seed viability-related traits. These findings provide the basis for the seed-based cloning and functional identification of related candidate genes for seed vigor.

Mapping the A Genome for QTL Conditioning Resistance to Fusarium Head Blight in a Wheat Population with Triticum timopheevii Background

Development and use of resistant wheat cultivars is the most practical and economical approach for the control of Fusarium head blight (FHB). In the present study, a population of recombinant inbred lines derived from the cross between ‘AC Brio’ (a Canadian bread wheat cultivar moderately susceptible to FHB) and ‘TC 67’ (an FHB-resistant cultivar derived from Triticum timopheevii) was used to map quantitative trait loci (QTL) for FHB resistance using microsatellite molecular markers. Multiple interval mapping detected several QTL for FHB resistance on the chromosomes 5AL and 6A. The QTL detected in the marker interval of cfd6.1-barc48 on chromosome 5AL explained 10.9, 5.2, and 7.8% of phenotypic variation for disease incidence (type I resistance), disease severity (a combination of type I and type II resistance), and Fusarium-damaged kernels (FDK) (type IV resistance) under field conditions, respectively. The second QTL mapped to 5AL, in the marker interval of cfd39-cfa2185, explained 19.4 and 20.6% of phenotypic variation for FDK under field conditions and disease severity in the greenhouse (type II resistance), respectively. The QTL located on chromosome 6A conferred resistance to disease incidence and severity under field conditions and to disease severity in the greenhouse, explaining 6.8 to 11.8% of phenotypic variation for these traits. Several QTL for agronomic traits were also mapped in this study, including one and two QTL to the chromosomes 2A and 5AL, respectively, all for plant height, and two QTL to chromosome 6A for plant height and flowering date, respectively. The 5AL QTL for FHB resistance mapped in the marker interval of cfd39-cfa2185 in the present study is a novel QTL that originated from T. timopheevii and is reported here for the first time. Further validation of this QTL is required for wheat breeding programs to enhance resistance levels to FHB.

Construction of a genetic linkage map in Lilium using a RIL mapping population based on SRAP marker

A genetic linkage map of lily was constructed using RILs (recombinant inbred lines) population of 180 individuals. This mapping population was developed by crossing Raizan No.1 (Formolongo) and Gelria (Longiflomm) cultivars through single-seed descent (SSD). SRAPs were generated by using restriction enzymes EcoRI in combination with either MseI. The resulting products were separated by electrophoresis on 6% denaturing polyacrylamide gel and visualized by silver staining. The segregation of each marker and linkage analysis was done using the program Mapmaker3.0. With 50 primer pairs, a total of 189 parental polymorphic bands were detected and 78 were used for mapping. The total map length was 2,135.5 cM consisted of 16 linkage groups. The number of markers in the linkage groups varied from 1 to 12. The length of linkage groups was range from 11.2 cM to 425.9 cM and mean marker interval distance range from 9.4 cM to 345.4 cM individually. The mean marker interval distance between markers was 27.4 cM. The map developed in the present study was the first sequence-related amplified polymorphism markers map of lily constructed with recombinant inbred lines, it could be used for genetic mapping and molecular marker assisted breeding and quantitative trait locus mapping of Lilium.

Upper Wenlock bentonites from Wren's Nest Hill, Dudley: comparisons with prominent bentonites along Wenlock Edge, Shropshire, England

The upper Wenlock Series (Homerian Stage) of the northern Midland Platform, England, contains numerous volcanic bentonite clay layers. At Wren's Nest Hill, Dudley, 15 bentonites have been investigated and comparisons with the type-Wenlock have been made by means of two key sections along Wenlock Edge, Shropshire. In total 22 bentonites have been investigated and their clay and sand-grade mineralogies determined. Rare earth element (REE) and yttrium concentrations of apatite grains contained within ten of the bentonites have been established allowing geochemical fingerprinting as an indication of provenance of source magmas and identification of geochemical marker beds. Based on the analysis of REE and yttrium concentrations it seems likely that the majority of these bentonites originated from a granodiorite magmatic source. Comparisons with published Llandovery and lower Wenlock age bentonites indicate generally more enrichment in light REEs relative to heavy REEs. In addition, close geochemical similarities between bentonites along Wenlock Edge and at Wren's Nest Hill strongly argue for their presence as precise stratigraphic equivalents within the upper Much Wenlock Limestone Formation. These correlations are further supported by geophysical data from borehole wire-line logs across the West Midlands. Finally, a chemically distinct mid-Homerian episode of volcanism is identified and represents a potentially important marker interval between the study area and other similarly aged bentonites reported from the Island of Gotland, Sweden.

An investigation of the power for separating closely linked QTL in experimental populations

SummaryHu & Xu (2008) developed a statistical method for computing the statistical power for detecting a quantitative trait locus (QTL) located in a marker interval. Their method is based on the regression interval mapping method and allows experimenters to effectively investigate the power for detecting a QTL in a population. This paper continues to work on the power analysis of separating multiple-linked QTLs. We propose simple formulae to calculate the power of separating closely linked QTLs located in marker intervals. The proposed formulae are simple functions of information numbers, variance inflation factors and genetic parameters of a statistical model in a population. Both regression and maximum likelihood interval mappings suitable for detecting QTL in the marker intervals are considered. In addition, the issue of separating linked QTLs in the progeny populations from an F2 subject to further self and/or random mating is also touched upon. One of the primary keys to our approach is to derive the genotypic distributions of three and four loci for evaluating the correlation structures between pairwise unobservable QTLs in the model across populations. The proposed formulae allow us to predict the power of separation when several factors, such as sample sizes, sizes and directions of QTL effects, distances between QTLs, interval sizes and relative QTL positions in the intervals, are considered together at a time in different experimental populations. Numerical justifications and Monte Carlo simulations were provided for confirmation and illustration.

Addition of Restriction Fragment Length Polymorphism Markers to the Genetic Linkage Map of Brassica rapa L. (syn. campestris)

Genetic linkage analysis of 151 restriction fragment length polymorphism (RFLP) loci, that included eight new loci, detected by the six probes in the present study, and four trait loci including seed colour, leaf pubescence, resistance to white rust caused by Albugo candida race-2 (AC-2) and race-7 (AC-7) employing the MAPMAKER/EXP 3.0 programme led to the development of 10 linkage groups (LGs) spanning over 44.4 centiMorgan (cM) to 130.4 cM containing 9 to 22 loci and two short LGs with two or three marker loci in Brassica rapa. The enriched map covers 993.1 cM of B. rapa genome with an average marker interval of 6.41. Eight new RFLP loci occupied new map positions on five linkage groups, LG 2, 3, 6, 8 and 9. Addition of these RFLP loci led to appreciable changes in the corresponding linkage groups and resulted in an increase of the total map length by 102.8 cM and of the marker interval by 0.35 cM. Interval mapping by using the computer programme MAPMAKER/ QTL 1.1 for scanning the genetic map led to the detection of one major quantitative trait locus (QTL) in LG 4 and one minor QTL in LG 8 governing resistance to AC-7. Both QTLs contributed 7.89 to the interaction phenotype (IP) score with 96.3% genetic variation. The multi-locus model suggested additive gene action with 96.8% genetic variation.