Recombinant Inbred Line Mapping Population Research Articles

High-resolution mapping of quantitative trait loci controlling main floral stalk length in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

BackgroundFor spring-type Chinese cabbage production, premature bolting refers to the excessive elongation of dwarf stems before harvesting. Although quantitative trait loci (QTL) mapping for bolting-related traits have been studied extensively, the main flower stalk length (MFSL) have been rarely investigated. Two inbred lines, 06–247 and He102, have significant differences in the MFSL. In this study, these two materials were selected as parental lines for the construction of a recombinant inbred line (RIL) mapping population. High-density mapping of QTL for the MFSL was performed based on the deep resequencing of parental lines and specific locus-amplified fragment sequencing (SLAF-Seq) of individual recombination inbred lines.ResultsAn F7 population consisting of 150 lines was developed. Deep resequencing of parental lines produced 21.08 gigabases, whereas SLAF-Seq produced an average of 428.35 million bases for each progeny. The total aligned data from the parental lines identified 1,082,885 high-quality single nucleotide polymorphisms (SNPs) between parental lines. Out of these, 5392 SNP markers with a segregation type of aa×bb and average integrity of > 99% were suitable for the genetic linkage map construction. The final map contained 10 linkage groups (LGs) was 1687.82 cM in length with an average distance of 0.32 cM between adjacent markers. Based on the high-density map, nine QTLs for MFSL were found to be distributed on seven chromosomes, and two major-effect QTLs were identified for the first time. The physical distance between adjacent markers of two major-effect QTLs was 44.37 kbp and 121.91 kbp, respectively. Approximately 2056 and 6769 SNP markers within confidence intervals were identified according to the results of parental line resequencing, which involved 24 and 199 mutant genes.ConclusionsThe linkage map constructed in this study has the highest density in Chinese cabbage to date. Two major-effect QTLs for MFSL in Chinese cabbage were also identified. Among these, a novel QTL associated with bolting mapped on LG A04 was identified based on MFSL. The results of this study provide an important platform for gene/QTL mapping and marker-assisted selection (MAS) breeding for bolting-resistant Chinese cabbage.

Twenty-four alleles at twelve quantitative trait loci act additively to control tiller angle in cultivated rice

Tiller angle, controlled by quantitative trait loci (QTL), is crucial for achieving ideal plant architecture in rice, which affects its final yield values. It is important to understand the genetic mechanisms underlying tiller angle when breeding new plant-type varieties. To uncover the genetic regulation mechanisms in cultivated rice, we performed QTL analysis using a recombinant inbred line (RIL) mapping population consisting of 219 lines developed by crossing two rice cultivars, Lemont and Yangdao4. The angle between the side tiller (ST) and the horizontal ground was measured as a tiller angle-related trait in QTL analysis. Twenty-three QTLs responsible for ST-ground angle were detected using multiple interval mapping in four mapping environments. A major QTL, qTA9, was detected on chromosome 9, which explained 12.9, 39.8, 37.9, and 28.3% of the phenotypic variation in the four mapping environments, respectively. Another QTL, qTA8, with a relatively large effect, was detected on chromosome 8. The other 21 QTLs explained < 10% of the phenotypic variation individually. These 23 detected QTLs were localized in 12 loci that act additively to influence tiller angle as demonstrated by regression analysis: plants carrying more ST-ground angle-increasing alleles at the 12 loci had larger ST-ground angles than those carrying more angle-decreasing alleles. Multiple comparison tests indicated that if marker-assisted selection was used in breeding, selecting five loci randomly from the 12 loci was enough to guarantee a phenotype with a ST-ground angle of over 78°. These results reveal the sophisticated genetic mechanisms controlling tiller angle in cultivated rice.

Characterization of terminal heat tolerance in bread wheat (Triticum aestivum L.) using differences in agronomic traits as potential selection criteria

The present study was undertaken to determine effectiveness of selection for genotypes tolerant to heat stress using differences in tiller per plant (dTPP), grain weight per plant (dGWPP), grain number per plant (dGNPP), biomass per plant (dBMPP) and spike length (dSL) under the optimum and late sown field condition. A Recombinant Inbred Line (RIL) mapping population derived from the heat sensitive genotype Raj 4014 and heat tolerant genotype WH730 was evaluated for the heat stress over 2 years in a replicated trial under optimum or timely (TS) and late sown (LS) field conditions. Parents and their RILs clearly showing variation with respect to the dTPP, dGWPP, dGNPP, dBMPP and dSL. There was differential response of genotypes under LS as compared to the TS. The field data recorded under precision planting using the dibbling method was very effective in capturing the data under both conditions. Considering the two sowing condition viz., LS and TS, mean of difference in tiller per plant (dTPP) was 1.64. While for grain no. per plant (dGNPP) and grain weight per plant (dGWPP), the mean differences observed between TS and LS were 76.55 and 3.02 g respectively. Difference in spike length (dSL) was 1.09 cm and biomass per plant (dBMPP) showed difference of 8.41 g.

Identification of QTL Associated with Drought Tolerance in Andean Common Bean

Drought stress is becoming one of the most important abiotic factors limiting productivity of common bean (Phaseolus vulgarisL.) globally. The objective of this study was to conduct a quantitative trait loci (QTL) analysis of drought tolerance in a recombinant inbred line (RIL) mapping population genotyped using single nucleotide polymorphism (SNP) markers. The RIL population was developed by crossing Portillo × Red Hawk, two Andean bean genotypes contrasting in reaction to drought stress and evaluated at two locations in Uganda for two seasons under drought stress (DS) and non‐stress (NS) conditions. Eighteen significant QTL signals were identified for phenology, yield component and partitioning traits on chromosomes Pv01, Pv02, Pv03, Pv04, Pv06, and Pv11 under DS and NS conditions. Quantitative trait loci for seed yield per plant (SY) were detected on Pv01, Pv02, Pv03, Pv04, and Pv06 under DS conditions. Colocalized QTL signals for pod weight per plant and SY were identified under DS on Pv01 (45.15 Mb) and on Pv02 (0.12 Mb), for phenology and SY on Pv03 near marker ss715639424 (40.16 Mb), and for SY and harvest index on Pv06 (17.92 Mb). Two candidate genes related to flowering were identified within a 35‐kb region from the ss715639424 marker on Pv03. GenePhvul.003G189100(30.3 kb) encodes “AGAMOUS‐LIKE 65 (AGL65),” which is essential for pollen development, and genePhvul.003G189300(17.9 kb) encodes “CYCLING DOF FACTOR 3 (CDF3)” that regulates flowering time. The same SY QTL, SY3.3PRon Pv03, was previously detected in Mesoamerican germplasm and could be used through marker‐assisted breeding to improve SY of Andean beans grown under DS.

QTL for spike-layer uniformity and their influence on yield-related traits in wheat

BackgroundCommon wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat spike-layer uniformity related traits (SLURTs) were complex traits that directly affect yield potential and appearance. In this study, quantitative trait locus (QTL) for five SLURTs among inter-tillers were first documented using a recombinant inbred line (RIL) mapping population derived from a cross between Kenong9204 and Jing411 (represented by KJ-RILs). Genetic relationships between SLURTs and yield were characterized in detail.ResultsThe trait phenotypic performances for the 188 KJ-RILs and their parents were evaluated in eight different environments. The genetic data included in a high-density genetic map derived from the Affymetrix 660 K SNP Array and the corresponding genotypes in each lines. Of 99 putative additive QTL 11 were stable across environments and 57 showed significant additive-by-environment interaction effects. These QTL individually explained 1.05–39.62% of the phenotypic variance, with log of odds (LOD) values ranging from 2.00 to 34.01. Genetic relationships between SLURTs and yield indicated that plants with slight uneven spike spatial distribution should be an ideotype for super high-yield in wheat.ConclusionsThe present study will provide assistance in understanding the genetic relationships between SLURTs and yield potential. The 11 stable QTL for SLURTs identified herein may facilitate breeding new wheat varieties with scientifically reasonable spike-layer distribution by marker assisted selection.

Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea.

Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F6-derived recombinant inbred line mapping populations for genetic analysis of resistance. The Yorker × Genesis114 (YG), Rupali × 04067-81-2-1-1 (RB) and Yorker × 04067-81-2-1-1 (YB) populations were genotyped using genotyping-by-sequencing and phenotyped for PRR under three field environments with a mixture of 10 P. medicaginis isolates. Whole-genome QTL analysis identified major QTL QRBprrsi01, QYBprrsi01, QRBprrsi03 and QYBprrsi02 for PRR resistance on chromosomes 3 and 6, in RB and YB populations, respectively, with the resistance source derived from the wild Cicer species. QTL QYGprrsi02 and QYGprrsi03 were also identified on chromosomes 5 and 6 in YG population from C. arietinum. Aligning QTL regions to the corresponding chickpea reference genome suggested that the resistance source from C. arietinum and C. echinospermum may be different. The findings from this study provide tools for marker-assisted selection in chickpea breeding and information to assist the development of populations suitable for fine-mapping of resistance loci to determine the molecular basis for PRR resistance in chickpea.

Identification and validation of QTL and their associated genes for pre-emergent metribuzin tolerance in hexaploid wheat (Triticum aestivum L.)

BackgroundHerbicide tolerance is an important trait that allows effective weed management in wheat crops. Genetic knowledge of metribuzin tolerance in wheat is needed to develop new cultivars for the industry. Here, we evaluated metribuzin tolerance in a recombinant inbred line (RIL) mapping population derived from Synthetic W7984 and Opata 85 over two consecutive years to identify quantitative trait loci (QTL) contributing to the trait. Herbicide tolerance was measured by two chlorophyll traits, SPAD chlorophyll content index (CCI) and visual senescence score (SNS). The markers associated with major QTL from Synthetic W7984, positively contributing to reduced phytotoxic effects under herbicide treatment were validated in two F3/4 recombinant inbred populations developed from crosses of Synthetic W7984 × Westonia and Synthetic W7984 × Lang.ResultsComposite interval mapping (CIM) identified four QTL, two on chromosome 4A and one each on chromosomes 2D and 1A. The chromosomal position of the two QTL mapped on 4A within 10 cM intervals was refined and validated by multiple interval mapping (MIM). The major QTL affecting both measures of tolerance jointly explained 42 and 45% of the phenotypic variation by percentage CCI reduction and SNS, respectively. The identified QTL have a pure additive effect. The metribuzin tolerant allele of markers, Xgwm33 and Xbarc343, conferred lower phytotoxicity and explained the maximum phenotypic variation of 28.8 and 24.5%, respectively. The approximate physical localization of the QTL revealed the presence of five candidate genes (ribulose-bisphosphate carboxylase, oxidoreductase (rbcS), glycosyltransferase, serine/threonine-specific protein kinase and phosphotransferase) with a direct role in photosynthesis and/or metabolic detoxification pathways.ConclusionMetribuzin causes photo-inhibition by interrupting electron flow in PSII. Consequently, chlorophyll traits enabled the measure of high proportion of genetic variability in the mapping population. The validated molecular markers associated with metribuzin tolerance mediating QTL may be used in marker-assisted breeding to select metribuzin tolerant lines. Alternatively, validated favourable alleles could be introgressed into elite wheat cultivars to enhance metribuzin tolerance and improve grain yield in dryland farming for sustainable wheat production.

Genetic mapping of ovary colour and quantitative trait loci for carotenoid content in the fruit of Cucurbita maxima Duchesne

The high content of carotenoids, sugars, dry matter, vitamins and minerals makes the fruit of winter squash (Cucurbita maxima Duchesne) a valuable fresh-market vegetable and an interesting material for the food industry. Due to their nutritional value, long shelf-life and health protective properties, winter squash fruits have gained increased interest from researchers in recent years. Despite these advantages, the genetic and genomic resources available for C. maxima are still limited. The aim of this study was to use the genetic mapping approach to map the ovary colour locus and to identify the quantitative trait loci (QTLs) for high carotenoid content and flesh colour. An F6 recombinant inbred line (RIL) mapping population was developed and used for evaluations of ovary colour, carotenoid content and fruit flesh colour. SSR markers and DArTseq genotyping-by-sequencing were used to construct an advanced genetic map that consisted of 1824 molecular markers distributed across linkage groups corresponding to 20 chromosomes of C. maxima. Total map length was 2208 cM and the average distance between markers was 1.21 cM. The locus affecting ovary colour was mapped at the end of chromosome 14. The identified QTLs for carotenoid content in the fruit and fruit flesh colour shared locations on chromosomes 2, 4 and 14. QTLs on chromosomes 2 and 4 were the most meaningful. A correlation was clearly confirmed between fruit flesh colour as described by the chroma value and carotenoid content in the fruit. A high-density genetic map of C. maxima with mapped loci for important fruit quality traits is a valuable resource for winter squash improvement programmes.

Genetic mapping of psl locus and quantitative trait loci for angular leaf spot resistance in cucumber (Cucumis sativus L.)

One of the most important cucumber diseases is bacterial angular leaf spot (ALS), whose increased occurrence in open-field production has been observed over the last years. To map ALS resistance genes, a recombinant inbred line (RIL) mapping population was developed from a narrow cross of cucumber line Gy14 carrying psl resistance gene and susceptible B10 line. Parental lines and RILs were tested under growth chamber conditions as well as in the field for angular leaf spot symptoms. Based on simple sequence repeat and DArTseq, genotyping a genetic map was constructed, which contained 717 loci in seven linkage groups, spanning 599.7 cM with 0.84 cM on average between markers. Monogenic inheritance of the lack of chlorotic halo around the lesions, which is typical for ALS resistance and related with the presence of recessive psl resistance gene, was confirmed. The psl locus was mapped on cucumber chromosome 5. Two major quantitative trait loci (QTL) psl5.1 and psl5.2 related to disease severity were found and located next to each other on chromosome 5; moreover, psl5.1 was co-located with psl locus. Identified QTL were validated in the field experiment. Constructed genetic map and markers linked to ALS resistance loci are novel resources that can contribute to cucumber breeding programs.

Registration of a Bread Wheat Recombinant Inbred Line Mapping Population Derived from a Cross Between ‘Harry’ and ‘Wesley’

The hard red winter wheat (Triticum aestivum L.) ‘Harry’ × ‘Wesley’ mapping population (Reg. No. MP‐9, NSL 523949 MAP) consists of 203 recombinant inbred lines and was developed at the University of Nebraska, Lincoln. The mapping population (F6:11) was derived from a cross between Harry (drought tolerant) and Wesley (drought susceptible) wheat cultivars using the single‐seed descent method. The primary goal in developing this mapping population was to identify genomic regions associated with agronomic traits in response to drought in the Harry and Wesley cultivars. The population segregates for a number of traits, including chaff color, leaf waxiness, flowering date, plant height, grain yield, yield component traits, and resistance to tan spot. A wide range of phenotypic diversity among individuals and transgressive segregation were observed for all segregating traits. The mapping population was genotyped using the genotyping‐by‐sequencing approach, and a high‐density linkage map developed. The quality and accuracy of the linkage map have been confirmed by mapping known genomic regions for two highly heritable traits, chaff color and leaf cuticular wax. The mapping population is an important germplasm resource that will provide wheat breeders with a diverse set of lines in combination with a high‐density genetic map that can be utilized to identify genomic regions at high mapping resolution and breed for drought tolerance and wider adaptation in the US Great Plains.

An Immortalized Genetic Mapping Population for Perennial Ryegrass: A Resource for Phenotyping and Complex Trait Mapping.

To address the lack of a truly portable, universal reference mapping population for perennial ryegrass, we have been developing a recombinant inbred line (RIL) mapping population of perennial ryegrass derived via single seed descent from a well-characterized F2 mapping population based on genetically distinct inbred parents in which the natural self-incompatibility (SI) system of perennial ryegrass has been overcome. We examined whether it is possible to create a genotyping by sequencing (GBS) based genetic linkage map in a small population of the F6 generation of this population. We used 41 F6 genotypes for GBS with PstI/MspI-based libraries. We successfully developed a genetic linkage map comprising 6074 SNP markers, placing a further 22080 presence and absence variation (PAV) markers on the map. We examined the resulting genetic map for general and RIL specific features. Overall segregation distortion levels were similar to those experienced in the F2 generation, but segregation distortion was reduced on linkage group 6 and increased on linkage group 7. Residual heterozygosity in the F6 generation was observed at a level of 5.4%. There was a high proportion of chromosomes (30%) exhibiting the intact haplotype of the original inbred parents of the F1 genotype from which the population is derived, pointing to a tendency for chromosomes to assort without recombining. This could affect the applicability of these lines and might make them more suitable for situations where repressed recombination is an advantage. Inter- and intra-chromosomal linkage disequilibrium (LD) analysis suggested that the map order was robust. We conclude that this RIL population, and subsequent F7 and F8 generations will be useful for genetic analysis and phenotyping of agronomic and biological important traits in perennial ryegrass.

Characterization and mapping of leaf rust resistance in four durum wheat cultivars.

Widening the genetic basis of leaf rust resistance is a primary objective of the global durum wheat breeding effort at the International Wheat and Maize Improvement Center (CIMMYT). Breeding programs in North America are following suit, especially after the emergence of new races of Puccinia triticina such as BBG/BP and BBBQD in Mexico and the United States, respectively. This study was conducted to characterize and map previously undescribed genes for leaf rust resistance in durum wheat and to develop reliable molecular markers for marker-assisted breeding. Four recombinant inbred line (RIL) mapping populations derived from the resistance sources Amria, Byblos, Geromtel_3 and Tunsyr_2, which were crossed to the susceptible line ATRED #2, were evaluated for their reaction to the Mexican race BBG/BP of P. triticina. Genetic analyses of host reactions indicated that leaf rust resistance in these genotypes was based on major seedling resistance genes. Allelism tests among resistant parents supported that Amria and Byblos carried allelic or closely linked genes. The resistance in Geromtel_3 and Tunsyr_2 also appeared to be allelic. Bulked segregant analysis using the Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified two genomic regions for leaf rust resistance; one on chromosome 6BS for Geromtel_3 and Tunsyr_2 and the other on chromosome 7BL for Amria and Byblos. Polymorphic SNPs identified within these regions were converted to kompetitive allele-specific PCR (KASP) assays and used to genotype the RIL populations. KASP markers usw215 and usw218 were the closest to the resistance genes in Geromtel_3 and Tunsyr_2, while usw260 was closely linked to the resistance genes in Amria and Byblos. DNA sequences associated with these SNP markers were anchored to the wild emmer wheat (WEW) reference sequence, which identified several candidate resistance genes. The molecular markers reported herein will be useful to effectively pyramid these resistance genes with other previously marked genes into adapted, elite durum wheat genotypes.

Identification of QTLs associated with heat tolerance at the heading and flowering stage in rice (Oryza sativa L.)

The ongoing rise in temperatures caused by global climate change is a critical climatic risk factor for rice production, and enhancing rice heat tolerance is an area of particular research interest. A recombinant inbred line (RIL) mapping population was developed from heat sensitive, rice cultivar IAPAR-9 crossed with heat tolerant, Liaoyan241. RIL and parental lines were exposed to high temperature at the heating and flowering stage in experiments in 2014 and 2015. As indicators of heat tolerance, the seed setting rate under natural (NS) and heat stress (HTS) conditions were measured, and the reduction rate of seed set (RRS) was calculated. Quantitative trait loci (QTL) analysis revealed eleven heat tolerance QTLs located on chromosomes 1, 3, 4, 5, and 6. Single QTL contribution rates were 4.75–13.81% and effect values were − 5.98 to 5.00. Four major QTLs (qNS1, qNS4, qNS6, and qRRS1) were stable detected in different environments in both years. Thirteen QTLs with epistatic interactions and nine QTLs with environmental interactions were also detected. Major QTLs were all involved in epistatic and environmental interactions. Three QTLs from the SSR marker interval RM471 to RM177 region of chromosome 4 (qNS4, qHTS4, and qRRS4) were all involved in epistatic and environmental interactions and contributed to phenotypic variation, indicating that this region constituted a major QTL hotspot. The major QTL for heat tolerance identified in this study will aid in breeding tolerant cultivars and facilitating investigation of the molecular underpinnings of heat tolerance in rice.

High-fidelity detection of crop biomass quantitative trait loci from low-cost imaging in the field.

Field‐based, rapid, and nondestructive techniques for assessing plant productivity are needed to accelerate the discovery of genotype‐to‐phenotype relationships in next‐generation biomass grass crops. The use of hemispherical imaging and light attenuation modeling was evaluated against destructive harvest measures with respect to their ability to accurately capture phenotypic and genotypic relationships in a field‐grown grass crop. Plant area index (PAI) estimated from below‐canopy hemispherical images, as well as a suite of thirteen traits assessed by manual destructive harvests, were measured in a Setaria recombinant inbred line mapping population segregating for aboveground productivity and architecture. A significant correlation was observed between PAI and biomass production across the population at maturity (r 2 = .60), as well as for select diverse genotypes sampled repeatedly over the growing season (r 2 = .79). Twenty‐seven quantitative trait loci (QTL) were detected for manually collected traits associated with biomass production. Of these, twenty‐one were found in four clusters of colocalized QTL. Analysis of image‐based estimates of PAI successfully identified all four QTL hot spots for biomass production. QTL for PAI had greater overlap with those detected for traits associated with biomass production than with those for plant architecture and biomass partitioning. Hemispherical imaging is an affordable and scalable method, which demonstrates how high‐throughput phenotyping can identify QTL related to biomass production of field trials in place of destructive harvests that are labor, time, and material intensive.

Registration of the Louise/Alpowa Wheat Recombinant Inbred Line Mapping Population

A mapping population was developed from the cross of soft white spring wheat (Triticum aestivum L.) cultivars ‘Louise’ and ‘Alpowa’ for use in investigating the genetic architecture of drought tolerance in the US Pacific Northwest. The Louise/Alpowa (Reg. No. MP‐8, NSL 520824 MAP) recombinant inbred line mapping population was developed through single seed descent from the F2 generation to the F5 generation. The population consists of 141 F5:6 recombinant inbred lines, of which 132 were used to construct the genetic linkage map. The 32 linkages groups included 882 single nucleotide polymorphism markers and one simple sequence repeat marker spanning 18 of 21 chromosomes. The Louise/Alpowa population was characterized for variation in agronomic traits, phenology, and end‐use quality traits. This population will be used for identification and introgression of multiple loci providing resistance to environmental stress such as drought, stripe rust, and high temperatures.

A consensus linkage map of lentil based on DArT markers from three RIL mapping populations.

BackgroundLentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes.Materials and methodsA consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including “CDC Redberry” x “ILL7502” (LR8), “ILL8006” x “CDC Milestone” (LR11) and “PI320937” x “Eston” (LR39).ResultsThe lentil consensus map was composed of 9,793 DArT markers, covered a total of 977.47 cM with an average distance of 0.10 cM between adjacent markers and constructed 7 linkage groups representing 7 chromosomes of the lentil genome. The consensus map had no gap larger than 12.67 cM and only 5 gaps were found to be between 12.67 cM and 6.0 cM (on LG3 and LG4). The localization of the SNP markers on the lentil consensus map were in general consistent with their localization on the three individual genetic linkage maps and the lentil consensus map has longer map length, higher marker density and shorter average distance between the adjacent markers compared to the component linkage maps.ConclusionThis high-density consensus map could provide insight into the lentil genome. The consensus map could also help to construct a physical map using a Bacterial Artificial Chromosome library and map based cloning studies. Sequence information of DArT may help localization of orientation scaffolds from Next Generation Sequencing data.

Putative Markers associated with Grain weight under Terminal Heat Stress in Bread-Wheat (Triticum aestivum L.)

Terminal heat tolerance is an important breeding target in wheat. Methods of selection for heat tolerance in wheat are limited. The most common approach is the evaluation of yield in nurseries grown under heat stress. The objective of this study was to estimate inheritance of heat tolerance and the grain character in bread wheat by combining molecular marker analysis. The tolerance in bread wheat using a cross between genotypes that were identified previously were utilized to identify SSR markers that are linked to traits associated with terminal heat tolerance. Grain wt. was used as a measure of heat tolerance because this trait was highly correlated with tolerance levels of genotypes. Genotypes WH730 and RAJ4014 were used as tolerant and sensitive parents respectively for generating mapping populations against the study of terminal heat stress respectively. A Recombinant Inbred Line (RIL) mapping population derived from the heat sensitive genotype RAJ4014 and heat tolerant genotype WH730 was evaluated for the heat stress over two years in a replicated trial under timely sown (TS) and late sown (LS) field conditions. The parental lines were screened with approximately 300 SSR (μsatellite) markers out of which about 20% showed polymorphism. Parents and their Recombinant inbred lines (RILs) screened by microsatellite markers for finding allelic variation. Xgwm48, Xgwm55 and Xcfd29 are three markers suggested an application of marker-assisted selection for wheat improvement under terminal heat tolerance.

New Method Application for Marker-Trait Association Studies in Plants: Partial Least Square Regression Aids Detection of Simultaneous Correlations.

In this work, we investigated the suitability of performing partial least square regression (PLSR) on genotype-phenotype datasets to identify marker-trait associations. We utilized data collected on a cotton (Gossypium hirsutum L.) recombinant inbred line (RIL) mapping population that was evaluated under contrasting irrigation treatments, well-watered and water-limited conditions, in a hot, arid environment in 2012. Two phenotypic data sets were used in combination with the genetic data which consisted of 841 marker loci assigned to 117 linkage groups. The first dataset contained canopy traits that were gathered using a mobile, high-throughput phenotyping platform and included canopy temperature (CT), normalized difference vegetation index (NDVI), and canopy height (CHT) with leaf area index (LAI) being derived from NDVI and CHT measurements. The second phenotypic data set consisted of 14 elemental concentration measurements corresponding to the following elements: P, K, Ca, Mn, Fe, Zn, Ni, Cu, As, Co, Rb, Mo, S, and Mg. To conduct the PSLR analyses we used the “pls” and “pls depot” available in R statistical software version 3.2.4. The PLSR bi plot from the analysis of the first dataset showed that three (LAI, NDVI, and CHT) out of the four canopy traits were highly correlated, and by using multivariate analysis of variance (MANOVA), we detected 22 significant (p<0.01) marker-trait associations for the four traits. In contrast to the canopy trait analysis, our PLSR bi plot for the second dataset showed varying correlations for each of the 14 traits. Because of the lack of distinct trait similarities, MANOVA was not an ideal option to test for marker-trait associations so we implemented a jackknife re sampling technique. Jackknife re sampling failed to detect significant marker effects for several of the 14 elemental concentration traits. Thus, our future work aims to test other re sampling techniques such as boot straping for traits that do not exhibit high correlation. Overall, PLSR was a very informative way to comprehend data structure, displaying correlations within markers, within traits, and between marker and traits in one bi plot. Further studies are still needed to leverage detection of additional variance in correlated datasets and to prevent spurious results. To the best of our knowledge, this is the first time PLSR has been reported in such a context.

Genetic dissection of plant growth habit in chickpea.

A combinatorial genomics-assisted breeding strategy encompassing association analysis, genetic mapping and expression profiling is found most promising for quantitative dissection of complex traits in crop plants. The present study employed GWAS (genome-wide association study) using 24,405 SNPs (single nucleotide polymorphisms) obtained with genotyping-by-sequencing (GBS) of 92 sequenced desi and kabuli accessions of chickpea. This identified eight significant genomic loci associated with erect (E)/semi-erect (SE) vs. spreading (S)/semi-spreading (SS)/prostrate (P) plant growth habit (PGH) trait differentiation regardless of diverse desi and kabuli genetic backgrounds of chickpea. These associated SNPs in combination explained 23.8% phenotypic variation for PGH in chickpea. Five PGH-associated genes were validated successfully in E/SE and SS/S/P PGH-bearing parental accessions and homozygous individuals of three intra- and interspecific RIL (recombinant inbred line) mapping populations as well as 12 contrasting desi and kabuli chickpea germplasm accessions by selective genotyping through Sequenom MassARRAY. The shoot apical, inflorescence and floral meristems-specific expression, including upregulation (seven-fold) of five PGH-associated genes especially in germplasm accessions and homozygous RIL mapping individuals contrasting with E/SE PGH traits was apparent. Collectively, this integrated genomic strategy delineated diverse non-synonymous SNPs from five candidate genes with strong allelic effects on PGH trait variation in chickpea. Of these, two vernalization-responsive non-synonymous SNP alleles carrying SNF2 protein-coding gene and B3 transcription factor associated with PGH traits were found to be the most promising in chickpea. The SNP allelic variants associated with E/SE/SS/S PGH trait differentiation were exclusively present in all cultivated desi and kabuli chickpea accessions while wild species/accessions belonging to primary, secondary and tertiary gene pools mostly contained prostrate PGH-associated SNP alleles. This indicates strong adaptive natural/artificial selection pressure (Tajima's D 3.15 to 4.57) on PGH-associated target genomic loci during chickpea domestication. These vital leads thus have potential to decipher complex transcriptional regulatory gene function of PGH trait differentiation and for understanding the selective sweep-based PGH trait evolution and domestication pattern in cultivated and wild chickpea accessions adapted to diverse agroclimatic conditions. Collectively, the essential inputs generated will be of profound use in marker-assisted genetic enhancement to develop cultivars with desirable plant architecture of erect growth habit types in chickpea.

Genetic Dissection of Novel QTLs for Resistance to Leaf Spots and Tomato Spotted Wilt Virus in Peanut (Arachis hypogaea L.).

Peanut is an important crop, economically and nutritiously, but high production cost is a serious challenge to peanut farmers as exemplified by chemical spray to control foliar diseases such as leaf spots and thrips, the vectors of tomato spotted wilt virus (TSWV). The objective of this research was to map the quantitative trait loci (QTLs) for resistance to leaf spots and TSWV in one recombinant inbred line (RIL) mapping population of “Tifrunner × GT-C20” for identification of linked markers for marker-assisted breeding. Here, we report the improved genetic linkage map with 418 marker loci with a marker density of 5.3 cM/loci and QTLs associated with multi-year (2010–2013) field phenotypes of foliar disease traits, including early leaf spot (ELS), late leaf spot (LLS), and TSWV. A total of 42 QTLs were identified with phenotypic variation explained (PVE) from 6.36 to 15.6%. There were nine QTLs for resistance to ELS, 22 QTLs for LLS, and 11 QTLs for TSWV, including six, five, and one major QTLs with PVE higher than 10% for resistance to each disease, respectively. Of the total 42 QTLs, 34 were mapped on the A sub-genome and eight mapped on the B sub-genome suggesting that the A sub-genome harbors more resistance genes than the B sub-genome. This genetic linkage map was also compared with two diploid peanut physical maps, and the overall co-linearity was 48.4% with an average co-linearity of 51.7% for the A sub-genome and 46.4% for the B sub-genome. The identified QTLs associated markers and potential candidate genes will be studied further for possible application in molecular breeding in peanut genetic improvement for disease resistance.