Interspecific Mapping Population Research Articles

Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data.

Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans.

Interspecific common bean population derived from Phaseolus acutifolius using a bridging genotype demonstrate useful adaptation to heat tolerance.

Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide and is a major nutrient source in the tropics. Common bean reproductive development is strongly affected by heat stress, particularly overnight temperatures above 20°C. The desert Tepary bean (Phaseolus acutifolius A. Gray) offers a promising source of adaptative genes due to its natural acclimation to arid conditions. Hybridization between both species is challenging, requiring in vitro embryo rescue and multiple backcrossing cycles to restore fertility. This labor-intensive process constrains developing mapping populations necessary for studying heat tolerance. Here we show the development of an interspecific mapping population using a novel technique based on a bridging genotype derived from P. vulgaris, P. Acutifolius and P. parvifolius named VAP1 and is compatible with both common and tepary bean. The population was based on two wild P. acutifolius accessions, repeatedly crossed with Mesoamerican elite common bush bean breeding lines. The population was genotyped through genotyping-by-sequencing and evaluated for heat tolerance by genome-wide association studies. We found that the population harbored 59.8% introgressions from wild tepary, but also genetic regions from Phaseolus parvifolius, a relative represented in some early bridging crosses. We found 27 significative quantitative trait loci, nine located inside tepary introgressed segments exhibiting allelic effects that reduced seed weight, and increased the number of empty pods, seeds per pod, stem production and yield under high temperature conditions. Our results demonstrate that the bridging genotype VAP1 can intercross common bean with tepary bean and positively influence the physiology of derived interspecific lines, which displayed useful variance for heat tolerance.

Mapping QTLs for yield and photosynthesis-related traits in three consecutive backcross populations of Oryza sativa cultivar Cottondora Sannalu (MTU1010) and Oryza rufipogon.

Identification of trait enhancing QTLs for yield and photosynthesis-related traits in rice using interspecific mapping population and chromosome segment substitution lines derived from a cross between Oryza sativa and Oryza rufipogon. Wild rice contains novel genes which can help in improving rice yield. Common wild rice Oryza rufipogon is a known source for enhanced photosynthesis and yield-related traits. We developed BC2F2:3:4 mapping populations using O. rufipogon IC309814 with high photosynthetic rate as donor, and elite cultivar MTU1010 as recurrent parent. Evaluation of 238 BC2F2 families for 13 yield-related traits and 208 BC2F2 families for seven photosynthesis-related physiological traits resulted in identification of significantly different lines which performed better than MTU1010 for various yield contributing traits. 49 QTLs were identified for 13 yield traits and 7 QTLs for photosynthesis-related traits in BC2F2. In addition, 34 QTLs in BC2F3 and 26 QTLs in BC2F4 were also detected for yield traits.11 common QTLs were identified in three consecutive generations and their trait-increasing alleles were derived from O. rufipogon. Significantly, one major effect common QTL qTGW3.1 for thousand grain weight with average phenotypic variance 8.1% and one novel QTL qBM7.1 for biomass were identified. Photosynthesis-related QTLs qPN9.1, qPN12.1, qPN12.2 qSPAD1.1 and qSPAD6.1 showed additive effect from O. rufipogon. A set of 145 CSSLs were identified in BC2F2 which together represented 87% of O. rufipogon genome. In addition, 87 of the 145 CSSLs were significantly different than MTU1010 for at least one trait. The major effect QTLs can be fine mapped for gene discovery. CSSLs developed in this study are a good source of novel alleles from O. rufipogon in the background of Cottondora Sannalu for rapid improvement of any trait in rice.

Inheritance and mapping of QTLs for Ascochyta blight resistance in chickpea (Cicer arietinum)

There are very limited studies on the QTLs governing Ascochyta blight resistance which is a major problem in chickpea (Cicer arietinum L.) grown in North West Plain Zone of India in the cooler climates and world over. An interspecific mapping population consisting of 157 F2:3 lines developed by crossing a resistant parent ILWC129 (C. reticulatum) with a susceptible variety GL769 (C. arietinum L.), was evaluated (2019–20) and genotyped (2021) for genetic studies and mapping of resistance to Ascochyta rabiei (syn. Phoma rabiei), isolate 8(3968). The inheritance pattern gave 1R:2H:1S goodness of fit ratio with χ2 value of 0.4 indicating that resistance against isolate 8 of the pathogen governed by a single gene. Out of 831 SSR markers screened, 86 were found polymorphic with 10.3% polymorphism from which only 41 markers segregated in 1:2:1 ratio and could be mapped. Eight linkage groups with a cumulative distance of 1042.31 cM were formed with an average distance of 25.42 cM. This is probably the first report of inheritance studies and tagging of A. rabei race 8 (arr8) resistance gene using molecular markers in an interspecific cross with C. reticulatum.

Genome Wide SNP Identification in <i>Eucalyptus</i> and its Application for Linkage Mapping and Adventitious Rooting Related QTL Analysis

Eucalyptus is a versatile genus with a particular significance for paper pulp, and it is extensively cultivated in India's marginal lands. Eucalyptus camaldulensis and E. tereticornis are highly preferred due to its optimal pulp yield, excellent fibre quality and good abiotic stress tolerance properties. Marker-assisted selections have played a major role in eucalyptus breeding programs. The use of genotyping-by-sequencing (GBS) approach for a largescale single nucleotide polymorphism (SNP) discovery and genotyping of an inter-specific mapping population, Eucalyptus tereticornis × E. camaldulensis are reported in this study. Reduced representation libraries of 81 F1 progeny were sequenced and number of SNPs considered for linkage analysis was 96,377 single nucleotide substitutions, most of which (54.03%) represented transition events. Totally, 1999 and 4206 SNP markers were mapped to female ( Eucalyptus tereticornis ) and male ( Eucalyptus camaldulensis ) map, respectively. Consensus map consisting of 4844 markers were placed on a linkage map, which spanned 1367.6 cM and had an average of one marker every 0.29 cM corresponding to a physical distance of about 0.66 Mb. The map was utilized to identify six quantitative trait loci (QTLs) associated with adventitious rooting traits of stem cuttings accounting for phenotypic variations ranging from 7.18% to 9.17%. Analysis of the genomic sequence corresponding to six QTLs led to the identification of 201 putative candidate genes and 4 key genes were related to adventitious rooting specific expression. The integrated strategy utilizing the identified QTLs along with the available genome could serve as a platform for candidate gene identification for molecular breeding of eucalypts.

High-Density Linkage Map Construction and QTL Identification in a Diploid Blueberry Mapping Population.

Genotyping by sequencing approaches have been widely applied in major crops and are now being used in horticultural crops like berries and fruit trees. As the original and largest producer of cultivated blueberry, the United States maintains the most diverse blueberry germplasm resources comprised of many species of different ploidy levels. We previously constructed an interspecific mapping population of diploid blueberry by crossing the parent F1#10 (Vaccinium darrowii Fla4B × diploid V. corymbosum W85–20) with the parent W85–23 (diploid V. corymbosum). Employing the Capture-Seq technology developed by RAPiD Genomics, with an emphasis on probes designed in predicted gene regions, 117 F1 progeny, the two parents, and two grandparents of this population were sequenced, yielding 131.7 Gbp clean sequenced reads. A total of 160,535 single nucleotide polymorphisms (SNPs), referenced to 4,522 blueberry genome sequence scaffolds, were identified and subjected to a parent-dependent sliding window approach to further genotype the population. Recombination breakpoints were determined and marker bins were deduced to construct a high density linkage map. Twelve blueberry linkage groups (LGs) consisting of 17,486 SNP markers were obtained, spanning a total genetic distance of 1,539.4 cM. Among 18 horticultural traits phenotyped in this population, quantitative trait loci (QTLs) that were significant over at least 2 years were identified for chilling requirement, cold hardiness, and fruit quality traits of color, scar size, and firmness. Interestingly, in 1 year, a QTL associated with timing of early bloom, full bloom, petal fall, and early green fruit was identified in the same region harboring the major QTL for chilling requirement. In summary, we report here the first high density bin map of a diploid blueberry mapping population and the identification of several horticulturally important QTLs.

Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population.

Wild soybean species (Glycine soja Siebold & Zucc.) comprise a unique resource to widen the genetic base of cultivated soybean [Glycine max (L.) Merr.] for various agronomic traits. An inter-specific mapping population derived from a cross of cultivar Williams 82 and PI 483460B, a wild soybean accession, was utilized for genetic characterization of root architecture traits. The objectives of this study were to identify and characterize quantitative trait loci (QTL) for seedling shoot and root architecture traits, as well as to determine additive/epistatic interaction effects of identified QTLs. A total of 16,469 single nucleotide polymorphisms (SNPs) developed for the Illumina beadchip genotyping platform were used to construct a high resolution genetic linkage map. Among the 11 putative QTLs identified, two significant QTLs on chromosome 7 were determined to be associated with total root length (RL) and root surface area (RSA) with favorable alleles from the wild soybean parent. These seedling root traits, RL (BARC_020495_04641 ~ BARC_023101_03769) and RSA (SNP02285 ~ SNP18129_Magellan), could be potential targets for introgression into cultivated soybean background to improve both tap and lateral roots. The RL QTL region harbors four candidate genes with higher expression in root tissues: Phosphofructokinase (Glyma.07g126400), Snf7 protein (Glyma.07g127300), unknown functional gene (Glyma.07g127900), and Leucine Rich-Repeat protein (Glyma.07g127100). The novel alleles inherited from the wild soybean accession could be used as molecular markers to improve root system architecture and productivity in elite soybean lines.

High-density genetic linkage map based on arbitrary and microsatellite markers using inter-specific recombinant inbred lines in eggplant (Solanum melongena L.)

Eggplant is an important Solanaceous vegetable crop with distinct morphological forms, colours, and shape of the fruits. Limited genomic coverage of the crop is a major constraint to unfold the cause of morphological variations underlying the contrasting traits. Therefore, with the aim to initiate targeted breeding efforts and to render ready-to-use markers for application in mapping quantitative trait loci (QTLs)/genes and to facilitate MAS, arbitrary and microsatellite molecular markers were used to map an inter-specific mapping population of 114 F8-recombinant inbred lines (RILs) developed using two contrasting lines, Ramnagar Giant (Solanum melongena L.) and W-4 (S. incanum L.). The arbitrary and microsatellite markers were screened for polymorphism with aim to cover the whole genome of eggplant. Of the total 1443 number of markers investigated, 6.07% RAPDs, 25% ISSR, 46.25% SCoT, and 22.46% SSRs revealed polymorphism between the parental lines, and were used for genotyping the RILs population. The results exhibit robust and sturdy nature of SCoT and microsatellite markers in unwrapping variations between both genotypes. Further, a high-density genetic linkage map was constructed with LOD threshold ≥ 4 clustered into 12 tentative linkage groups and spanning 1165 cM of the eggplant genome with an average marker density of 4.13 cM. The results shall further be used in mapping QTLs of agri-horticultural traits in eggplant.

Integrated genetic linkage maps for Korean pears (Pyrus hybrid) using GBS-based SNPs and SSRs

Integrated linkage maps are a valuable tool for comparative mapping between and within genus and species. Novel single-nucleotide polymorphism (SNP) linkage maps integrated with simple sequence repeats (SSRs) based on pseudo-chromosomes of the Chinese pear reference genome of ‘Dangshansuli’ (Pyrus bretschneideri) were constructed. In total, 4801 qualified SNP markers were obtained using a customized pipeline. The consensus map for ‘Whangkeumbae’ and ‘Minibae’ contained 321 SNP and 30 SSR markers spanning 1511.1 cM with an average genetic distance of 4.3 cM. A total of 30 SSR markers made it possible to compare our consensus map to other pear and apple maps. SSR markers originating from pear and apple maps showed high co-linearity. SNPs coordinated with pseudo-chromosomes, provide information on physical length coverage for 17 corresponding linkage groups, and enable easier genome annotation for genomic regions detected by quantitative trait loci analysis. Genotyping-by-sequencing-based SNP maps integrated with SSRs in the interspecific mapping population illustrate the genomic structure of Korean pear resources and will be used as our reference maps for tribe Maleae.

Mapping non-host resistance to the stem rust pathogen in an interspecific barberry hybrid

BackgroundNon-host resistance (NHR) presents a compelling long-term plant protection strategy for global food security, yet the genetic basis of NHR remains poorly understood. For many diseases, including stem rust of wheat [causal organism Puccinia graminis (Pg)], NHR is largely unexplored due to the inherent challenge of developing a genetically tractable system within which the resistance segregates. The present study turns to the pathogen’s alternate host, barberry (Berberis spp.), to overcome this challenge.ResultsIn this study, an interspecific mapping population derived from a cross between Pg-resistant Berberis thunbergii (Bt) and Pg-susceptible B. vulgaris was developed to investigate the Pg-NHR exhibited by Bt. To facilitate QTL analysis and subsequent trait dissection, the first genetic linkage maps for the two parental species were constructed and a chromosome-scale reference genome for Bt was assembled (PacBio + Hi-C). QTL analysis resulted in the identification of a single 13 cM region (~ 5.1 Mbp spanning 13 physical contigs) on the short arm of Bt chromosome 3. Differential gene expression analysis, combined with sequence variation analysis between the two parental species, led to the prioritization of several candidate genes within the QTL region, some of which belong to gene families previously implicated in disease resistance.ConclusionsFoundational genetic and genomic resources developed for Berberis spp. enabled the identification and annotation of a QTL associated with Pg-NHR. Although subsequent validation and fine mapping studies are needed, this study demonstrates the feasibility of and lays the groundwork for dissecting Pg-NHR in the alternate host of one of agriculture’s most devastating pathogens.

Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations.

A total of 132 domestication-related QTLs, of which 41 were novel, were identified through genotyping-by-sequencing of two Glycine max × Glycine soja populations. Soybean [Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja. The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger seeds, erect growth, larger stem diameter, reduced pod shattering, and altered growth habit. The objective of this study was to identify QTLs controlling key domestication-related traits (DRTs) using interspecific mapping populations. A total of 151 RILs from Williams 82 × PI 468916 and 510 RILs from Williams 82 × PI 479752 were utilized for QTL mapping. These lines were genotyped using a genotyping-by-sequencing protocol which resulted in approximately 5000 polymorphic SNP markers. The number of QTLs detected for each of the eleven DRTs ranged between 0-4 QTLs in the smaller Williams 82 × PI 468916 population and 3-16 QTLs in the larger Williams 82 × PI 479752 population. A total of 132 QTLs were detected, of which 51 are associated with selective sweeps previously related to soybean domestication. These QTLs were detected across all 20 chromosomes within 42 genomic regions. This study identifies 41 novel QTLs not detected in previous studies using smaller populations while also confirming the quantitative nature for several of the important DRTs in soybeans. These results would enable more effective use of the wild germplasm for soybean improvement.

Dissecting genomic hotspots underlying seed protein, oil, and sucrose content in an interspecific mapping population of soybean using high-density linkage mapping.

SummaryThe cultivated [Glycine max (L) Merr.] and wild [Glycine soja Siebold & Zucc.] soybean species comprise wide variation in seed composition traits. Compared to wild soybean, cultivated soybean contains low protein, high oil, and high sucrose. In this study, an interspecific population was derived from a cross between G. max (Williams 82) and G. soja (PI 483460B). This recombinant inbred line (RIL) population of 188 lines was sequenced at 0.3× depth. Based on 91 342 single nucleotide polymorphisms (SNPs), recombination events in RILs were defined, and a high‐resolution bin map was developed (4070 bins). In addition to bin mapping, quantitative trait loci (QTL) analysis for protein, oil, and sucrose was performed using 3343 polymorphic SNPs (3K‐SNP), derived from Illumina Infinium BeadChip sequencing platform. The QTL regions from both platforms were compared, and a significant concordance was observed between bin and 3K‐SNP markers. Importantly, the bin map derived from next‐generation sequencing technology enhanced mapping resolution (from 1325 to 50 Kb). A total of five, nine, and four QTLs were identified for protein, oil, and sucrose content, respectively, and some of the QTLs coincided with soybean domestication‐related genomic loci. The major QTL for protein and oil were mapped on Chr. 20 (qPro_20) and suggested negative correlation between oil and protein. In terms of sucrose content, a novel and major QTL were identified on Chr. 8 (qSuc_08) and harbours putative genes involved in sugar transport. In addition, genome‐wide association using 91 342 SNPs confirmed the genomic loci derived from QTL mapping. A QTL‐based haplotype using whole‐genome resequencing of 106 diverse soybean lines identified unique allelic variation in wild soybean that could be utilized to widen the genetic base in cultivated soybean.

A Multiple QTL-Seq Strategy Delineates Potential Genomic Loci Governing Flowering Time in Chickpea.

Identification of functionally relevant potential genomic loci using an economical, simpler and user-friendly genomics-assisted breeding strategy is vital for rapid genetic dissection of complex flowering time quantitative trait in chickpea. A high-throughput multiple QTL-seq strategy was employed in two inter (Cicer arietinum desi accession ICC 4958 × C reticulatum wild accession ICC 17160)- and intra (ICC 4958 × C. arietinum kabuli accession ICC 8261)-specific RIL mapping populations to identify the major QTL genomic regions governing flowering time in chickpea. The whole genome resequencing discovered 1635117 and 592486 SNPs exhibiting differentiation between early- and late-flowering mapping parents and bulks, constituted by pooling the homozygous individuals of extreme flowering time phenotypic trait from each of two aforesaid RIL populations. The multiple QTL-seq analysis using these mined SNPs in two RIL mapping populations narrowed-down two longer (907.1 kb and 1.99 Mb) major flowering time QTL genomic regions into the high-resolution shorter (757.7 kb and 1.39 Mb) QTL intervals on chickpea chromosome 4. This essentially identified regulatory as well as coding (non-synonymous/synonymous) novel SNP allelic variants from two efl1 (early flowering 1) and GI (GIGANTEA) genes regulating flowering time in chickpea. Interestingly, strong natural allelic diversity reduction (88–91%) of two known flowering genes especially mapped at major QTL intervals as compared to that of background genomic regions (where no flowering time QTLs were mapped; 61.8%) in cultivated vis-à-vis wild Cicer gene pools was evident inferring the significant impact of evolutionary bottlenecks on these loci during chickpea domestication. Higher association potential of coding non-synonymous and regulatory SNP alleles mined from efl1 (36–49%) and GI (33–42%) flowering genes for early and late flowering time differentiation among chickpea accessions was evident. The robustness and validity of two functional allelic variants-containing genes localized at major flowering time QTLs was apparent by their identification from multiple intra-/inter-specific mapping populations of chickpea. The functionally relevant molecular tags delineated can be of immense use for deciphering the natural allelic diversity-based domestication pattern of flowering time and expediting genomics-aided crop improvement to develop early flowering cultivars of chickpea.

A High-Resolution InDel (Insertion-Deletion) Markers-Anchored Consensus Genetic Map Identifies Major QTLs Governing Pod Number and Seed Yield in Chickpea.

Development and large-scale genotyping of user-friendly informative genome/gene-derived InDel markers in natural and mapping populations is vital for accelerating genomics-assisted breeding applications of chickpea with minimal resource expenses. The present investigation employed a high-throughput whole genome next-generation resequencing strategy in low and high pod number parental accessions and homozygous individuals constituting the bulks from each of two inter-specific mapping populations [(Pusa 1103 × ILWC 46) and (Pusa 256 × ILWC 46)] to develop non-erroneous InDel markers at a genome-wide scale. Comparing these high-quality genomic sequences, 82,360 InDel markers with reference to kabuli genome and 13,891 InDel markers exhibiting differentiation between low and high pod number parental accessions and bulks of aforementioned mapping populations were developed. These informative markers were structurally and functionally annotated in diverse coding and non-coding sequence components of genome/genes of kabuli chickpea. The functional significance of regulatory and coding (frameshift and large-effect mutations) InDel markers for establishing marker-trait linkages through association/genetic mapping was apparent. The markers detected a greater amplification (97%) and intra-specific polymorphic potential (58–87%) among a diverse panel of cultivated desi, kabuli, and wild accessions even by using a simpler cost-efficient agarose gel-based assay implicating their utility in large-scale genetic analysis especially in domesticated chickpea with narrow genetic base. Two high-density inter-specific genetic linkage maps generated using aforesaid mapping populations were integrated to construct a consensus 1479 InDel markers-anchored high-resolution (inter-marker distance: 0.66 cM) genetic map for efficient molecular mapping of major QTLs governing pod number and seed yield per plant in chickpea. Utilizing these high-density genetic maps as anchors, three major genomic regions harboring each of pod number and seed yield robust QTLs (15–28% phenotypic variation explained) were identified on chromosomes 2, 4, and 6. The integration of genetic and physical maps at these QTLs mapped on chromosomes scaled-down the long major QTL intervals into high-resolution short pod number and seed yield robust QTL physical intervals (0.89–2.94 Mb) which were essentially got validated in multiple genetic backgrounds of two chickpea mapping populations. The genome-wide InDel markers including natural allelic variants and genomic loci/genes delineated at major six especially in one colocalized novel congruent robust pod number and seed yield robust QTLs mapped on a high-density consensus genetic map were found most promising in chickpea. These functionally relevant molecular tags can drive marker-assisted genetic enhancement to develop high-yielding cultivars with increased seed/pod number and yield in chickpea.

Genetic linkage mapping of loci conferring resistance to Blue butterfly (Lampides boeticus L.) and Plume moth (Exelastis atomosa Wals.) on chromosome 2 (CcLG02) in Pigeonpea

Inheritance of host resistance to blue butterfly (PBB1) and plume moth (PPM1) in interspecific mapping populations (F2, F3 and BC1) derived from a cross involving Cajanus cajan (cv. ICP-26) × Cajanus scarabaeoides (acc. ICPW-94) appeared to be under monogenic control either by a single major gene or a cluster of tightly linked genes. Bulked segregant analysis using 237 [85 simple sequence repeats (SSR), 143 random amplified polymorphic DNA (RAPD) and nine inter simple sequence repeats (ISSR)] parental polymorphic primers led to the identification of 43 markers that distinguished the resistant and susceptible bulks alike to parents, and which were also segregating among F2 progenies. Linkage analysis of these markers along with interaction phenotype score for both traits generated a linkage group consisting of 11 markers (two SSR, seven RAPD and two ISSR) and two trait loci (PBB1 and PPM1). This linkage group distributed over 133.9 cM with an average marker interval of 10.3 cM. The PBB1 and PPM1 loci were linked to each other by 11.2 cM (rf 0.110), and were flanked by ISSR marker UBC8722000 (15.9 cM), and RAPD marker OPA09910 (15.3 cM), respectively. On the basis of sequence homology of linked marker OPA09910 these two loci were assigned to chromosome 2 (CcLG02). Composite interval mapping led to the detection of two major quantitative trait loci (qPBB2.1 and qPPM2.1) controlling blue butterfly and plume moth resistance, respectively and the quantitative trait locus peaks coinciding with PBB1 and PPM1 loci on the map.

MQTL-seq delineates functionally relevant candidate gene harbouring a major QTL regulating pod number in chickpea.

The present study used a whole-genome, NGS resequencing-based mQTL-seq (multiple QTL-seq) strategy in two inter-specific mapping populations (Pusa 1103 × ILWC 46 and Pusa 256 × ILWC 46) to scan the major genomic region(s) underlying QTL(s) governing pod number trait in chickpea. Essentially, the whole-genome resequencing of low and high pod number-containing parental accessions and homozygous individuals (constituting bulks) from each of these two mapping populations discovered >8 million high-quality homozygous SNPs with respect to the reference kabuli chickpea. The functional significance of the physically mapped SNPs was apparent from the identified 2,264 non-synonymous and 23,550 regulatory SNPs, with 8–10% of these SNPs-carrying genes corresponding to transcription factors and disease resistance-related proteins. The utilization of these mined SNPs in Δ (SNP index)-led QTL-seq analysis and their correlation between two mapping populations based on mQTL-seq, narrowed down two (CaqaPN4.1: 867.8 kb and CaqaPN4.2: 1.8 Mb) major genomic regions harbouring robust pod number QTLs into the high-resolution short QTL intervals (CaqbPN4.1: 637.5 kb and CaqbPN4.2: 1.28 Mb) on chickpea chromosome 4. The integration of mQTL-seq-derived one novel robust QTL with QTL region-specific association analysis delineated the regulatory (C/T) and coding (C/A) SNPs-containing one pentatricopeptide repeat (PPR) gene at a major QTL region regulating pod number in chickpea. This target gene exhibited anther, mature pollen and pod-specific expression, including pronounced higher up-regulated (∼3.5-folds) transcript expression in high pod number-containing parental accessions and homozygous individuals of two mapping populations especially during pollen and pod development. The proposed mQTL-seq-driven combinatorial strategy has profound efficacy in rapid genome-wide scanning of potential candidate gene(s) underlying trait-associated high-resolution robust QTL(s), thereby expediting genomics-assisted breeding and genetic enhancement of crop plants, including chickpea.

High resolution map of eggplant (Solanum melongena) reveals extensive chromosome rearrangement in domesticated members of the Solanaceae

A linkage map of eggplant was constructed for an interspecific F2 population derived from a cross between Solanum linnaeanum MM195 and S. melongena MM738. The map contains 400 AFLP® (amplified fragment length polymorphism), 348 RFLP (restriction fragment length polymorphism) and 116 COSII (conserved ortholog set) markers. The 864 mapped markers encompass 12 linkage groups, span 1,518 cM and are spaced at an average interval of 1.8 cM. Use of orthologous markers allowed confirmation of the established syntenic relationships between eggplant and tomato chromosomes and helped delineate the nature of the 33 chromosomal rearrangements and 11 transpositions distinguishing the two species. This genetic map provides a 2- to 3-fold improvement in marker density compared to previously published interspecific maps. Because the interspecific mapping population is rich in morphological variation, this greater genome saturation will be useful for QTL (quantitative trait locus) analyses. The recent release of the tomato genome sequence will provide additional opportunities for exploiting this map for comparative genomics and crop improvement.

Is it Possible to Combine High Content in Phenolics with Low Browning in Fruits and Vegetables? A case in Eggplant

Demand among consumers for fruits and vegetables with improved contents in bioactive compounds is increasing. In particular, a lot of attention is being paid to phenolic compounds, as they have been reported to present many beneficial effects for human health. However, oxidation of phenolic compounds present in the tissues of fruits and vegetables by polyphenol oxidases (PPOs) can result in browning, which affects negatively the quality of the produce. Eggplant ( Solanum melongena ) presents a high content in phenolics, in particular chlorogenic acid (CGA), which confers nutraceutical properties to this crop. In order to obtain information relevant for the development of varieties with high content in CGA and low browning, we have studied the diversity for CGA, PPO activity, and fruit flesh browning and their relationships in a collection of 18 Spanish accessions of eggplant. Also, using an interspecific mapping population between S. melongena and S. incanum we have mapped the genes involved in the synthesis pathway of CGA as well as the eggplant PPO genes. The results confirmed that eggplant presents high levels of CGA, and that a wide diversity exists for the three traits studied. Low levels of correlation have been found between CGA and PPO activity on one side and browning on the other, indicate that PPO is not a limiting factor in browning in the germplasm collection studied. The six genes of the pathway for the synthesis of CGA from phenylalanine have been mapped to five different linkage groups. Only two of the genes are linked indicating that selection of materials with the alleles favourable of different parents will be easily achieved. However, the five PPO genes mapped (PPO1 to PPO5) cluster together in the same linkage group, which will difficult obtaining recombinants. Mapping of these genes is of interest for marker assisted selection for high content in CGA and reduced browning. Overall, the results indicate that selection of eggplant varieties with high content in CGA and low browning is feasible. The information obtained is also useful for the genetic improvement of other fruits and vegetables in order to develop new cultivars with increased added value resulting from high content in phenolics and low browning.

Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP

Gossypium hirsutum and G. barbadense are two cultivated tetraploid cotton species with differences in fibre quality. The fibre of G. barbadense is longer, stronger and finer than that of G. hirsutum. To isolate genes expressed differently between the two species during fibre development, cDNA-SRAP (sequence-related amplified polymorphism) was applied. This technique was used to analyse genes at different stages of fibre development in G. hirsutum cv. Emian22 and G. barbadense acc. 3-79, the parents of our interspecific mapping population. A total of 4096 SRAP primer combinations were used to screen polymorphism between the DNA of the parents, and 275 highly polymorphic primers were picked out to analyse DNA and RNA from leaves and fibres at different developmental stages of the parents. A total of 168 DNA fragments were isolated from gels and sequenced: 54, 30, 38 and 41 from fibres of 5, 10, 15 and 20 days post-anthesis, respectively, and five from multi stages. To genetically map these sequences, 104 sequence-specific primers were developed and were used to screened polymorphism between the mapping parents. Finally, six markers were mapped on six chromosomes of our backbone interspecific genetic map. This work can give us a primary knowledge of differences in mechanism of fibre development between G. hirsutum and G. barbadense.

A genetic map of an interspecific diploid pseudo testcross population of coffee

Coffee is globally one of the most important export crops and is a prominent part of the economy in more than 50 countries in Latin America, Africa and Asia. In Colombia, it has been the leading export commodity for more than a century. However, genetic research on coffee has been rather sparse and mainly focused on the two major cultivated species, Coffea arabica L. and C. canephora P., leaving unexplored the genetic potential in other species. In this study, an interspecific mapping population consisting of 101 F1 hybrid plants from a cross between the diploid species C. liberica and C. eugenioides was evaluated for genetic segregation at 618 molecular marker loci. Of these, 168 SSRs and two ESTs exhibited polymorphic patterns that allowed segregation analysis and genetic linkage estimations. A genetic map consisting of 146 co-dominant loci and 11 predicted linkage groups was constructed using the mapping software JoinMap 3.0. The conjoined maternal/paternal map length is 798.68 cM, has an average saturation density of 6.01 cM/interval, and covers an estimated 66–86 % of the diploid coffee genome. Approximately 24 % of loci had null alleles, and 23.5 % exhibited segregation distortion. Knowledge derived from this study has important applications for quantitative trait locus analysis and marker-assisted selection in Colombian coffee breeding programs.