Recombinant Inbred Line Mapping Population Research Articles

A Genome-Wide mQTL-seq Scan Identifies Potential Molecular Signatures Regulating Plant Height in Chickpea

The current study employed a high-throughput genome-wide next-generation sequencing-led multiple QTL-seq (mQTL-seq) strategy in two inter- and intra-specific recombinant inbred line (RIL) mapping populations to identify the major genomic regions underlying robust quantitative trait loci (QTLs) regulating plant height in chickpea. The whole genome resequencing discovered 446,475 and 150,434 high-quality homozygous single nucleotide polymorphisms (SNPs) exhibiting polymorphism between tall and dwarf/semi-dwarf mapping parents and bulk/homozygous individuals selected from each of two chickpea RIL populations. These SNP-led mQTL-seq assays in RIL mapping populations scaled-down two longer major genomic regions (1.26–1.34 Mb) underlying robust plant height QTLs into the shorter high-resolution QTL intervals (653.2–756.3 kb) on chickpea chromosomes 3 and 8. This essentially delineated regulatory novel natural SNP allelic variants from brassinosteroid insensitive 1-receptor kinase 1 (BAK1) and gibberellin (GA) 20-oxidase genes governing plant height in chickpea. A strong impact of evolutionary bottlenecks including strong artificial/natural selection on two plant height gene loci during chickpea domestication was observed. The shoot apical meristem-specific expression aside from down-regulation of two plant height genes especially in dwarf/semi-dwarf as compared to tall parents and homozygous mapping individuals of two aforementioned RIL populations was apparent. The integrated genomics-assisted breeding strategy combining mQTL-seq with differential gene expression profiling and functional allelic diversity-based trait domestication study collectively identified potential natural allelic variants of candidate genes underlying major plant height QTLs in chickpea. These functionally relevant molecular signatures can be of immense use for marker-aided genetic enhancement to develop high seed- and pod-yielding non-lodging cultivars restructured with desirable plant height in chickpea.

Co-localization of major quantitative trait loci for pod size and weight to a 3.7\xa0cM interval on chromosome A05 in cultivated peanut (Arachis hypogaea L.)

BackgroundCultivated peanut (Arachis hypogaea L.), an important source of edible oil and protein, is widely grown in tropical and subtropical areas of the world. Genetic improvement of yield-related traits is essential for improving yield potential of new peanut varieties. Genomics-assisted breeding (GAB) can accelerate the process of genetic improvement but requires linked markers for the traits of interest. In this context, we developed a recombinant inbred line (RIL) mapping population (Yuanza 9102 × Xuzhou 68-4) with 195 individuals and used to map quantitative trait loci (QTLs) associated with three important pod features, namely pod length, pod width and hundred-pod weight.ResultsQTL analysis using the phenotyping data generated across four environments in two locations and genotyping data on 743 mapped loci identified 15 QTLs for pod length, 11 QTLs for pod width and 16 QTLs for hundred-pod weight. The phenotypic variation explained (PVE) ranged from 3.68 to 27.84%. Thirteen QTLs were consistently detected in at least two environments and three QTLs (qPLA05.7, qPLA09.3 and qHPWA05.6) were detected in all four environments indicating their consistent and stable expression. Three major QTLs, detected in at least three environments, were found to be co-localized to a 3.7 cM interval on chromosome A05, and they were qPLA05.7 for pod length (16.89–27.84% PVE), qPWA05.5 for pod width (13.73–14.12% PVE), and qHPWA05.6 for hundred-pod weight (13.75–26.82% PVE). This 3.7 cM linkage interval corresponds to ~2.47 Mb genomic region of the pseudomolecule A05 of A. duranensis, including 114 annotated genes related to catalytic activity and metabolic process.ConclusionsThis study identified three major consistent and stable QTLs for pod size and weight which were co-localized in a 3.7 cM interval on chromosome A05. These QTL regions not only offer further investigation for gene discovery and development of functional markers but also provide opportunity for deployment of these QTLs in GAB for improving yield in peanut.

Joint Linkage QTL Mapping for Yield and Agronomic Traits in a Composite Map of Three Common Bean RIL Populations

Bean (Phaseolus vulgaris L.) production is challenged by many limitations with drought being among the top causes of crop failure worldwide. In this study, we constructed three small‐red‐seeded bean recombinant inbred line (RIL) mapping populations (S48M, S94M, and S95M) with a common parent (‘Merlot’) and performed joint interval mapping analysis as a small nested association mapping (NAM) population for agronomic traits and performance under rainfed conditions in Michigan. The objective was to identify novel sources of improved performance and genomic regions associated with desirable traits under rainfed and water‐sufficient conditions in small‐red bean breeding materials adapted to temperate zones. A composite linkage map was constructed using single‐nucleotide polymorphism (SNP) markers from the three populations and resulted in an improved version of the individual linkage maps shown by a greater genome span covered in the composite map (909 cM). A number of quantitative trait loci (QTL) of different size effects were identified for seed yield (R2 = 15.4–30.7%), seed size (R2 = 16.4–20.2%), days to flowering (R2 = 12.4–36.1%), days to maturity (R2 = 16.2%), lodging score (R2 = 10.3–12.9%), and canopy height (R2 = 17%). Our study confirmed previously reported QTL on five chromosomes and identified a new QTL for canopy height on chromosome Pv10. The use of a composite map and QTL analysis under a NAM population structure increased our ability to detect small‐effect QTL that were segregating in at least two of the populations but would not have been detected using individual linkage maps.

Development of a High-Density Linkage Map and Tagging Leaf Spot Resistance in Pearl Millet Using Genotyping-by-Sequencing Markers.

Pearl millet [ (L.) R. Br; also (L.) Morrone] is an important crop throughout the world but better genomic resources for this species are needed to facilitate crop improvement. Genome mapping studies are a prerequisite for tagging agronomically important traits. Genotyping-by-sequencing (GBS) markers can be used to build high-density linkage maps, even in species lacking a reference genome. A recombinant inbred line (RIL) mapping population was developed from a cross between the lines 'Tift 99DB' and 'Tift 454'. DNA from 186 RILs, the parents, and the F was used for 96-plex KI GBS library development, which was further used for sequencing. The sequencing results showed that the average number of good reads per individual was 2.2 million, the pass filter rate was 88%, and the CV was 43%. High-quality GBS markers were developed with stringent filtering on sequence data from 179 RILs. The reference genetic map developed using 150 RILs contained 16,650 single-nucleotide polymorphisms (SNPs) and 333,567 sequence tags spread across all seven chromosomes. The overall average density of SNP markers was 23.23 SNP/cM in the final map and 1.66 unique linkage bins per cM covering a total genetic distance of 716.7 cM. The linkage map was further validated for its utility by using it in mapping quantitative trait loci (QTLs) for flowering time and resistance to leaf spot [ (Cke.) Sacc.]. This map is the densest yet reported for this crop and will be a valuable resource for the pearl millet community.

Identification of novel major and minor QTLs associated with Xanthomonas oryzae pv. oryzae (African strains) resistance in rice (Oryza sativa L.).

BackgroundXanthomonas oryzae pv. oryzae (Xoo) is the causal agent of Bacterial Leaf Blight (BB), an emerging disease in rice in West-Africa which can induce up to 50 % of yield losses. So far, no specific resistance gene or QTL to African Xoo were mapped. The objectives of this study were to identify and map novels and specific resistance QTLs to African Xoo strains.ResultsThe reference recombinant inbred lines (RIL) mapping population derived from the cross between IR64 and Azucena was used to investigate Xoo resistance. Resistance to African and Philippine Xoo strains representing different races was assessed on the RIL population under greenhouse conditions. Five major quantitative trait loci (QTL) for resistance against African Xoo were located on different chromosomes. Loci on chromosomes 1, 7, 9, 10 and 11 explained as much as 13 %, 37 %, 13 %, 11 % and 15 % of resistance variation, respectively. A major novel QTL located on chromosome 7 explained 37 % of the phenotypic variance to the African Xoo corresponding to race A3 whereas that on chromosome 11 is effective to all African races tested. Together with genes and QTLs for resistance to bacterial blight previously described, the QTLs described here were mapped onto the reference O. sativa subs japonica (var. Nipponbare) physical map.ConclusionWe characterized new resistance QTLs. While some co-localize with known resistance genes/QTLs to Asian strains, others are specific to African strains. We result with new information on genes and QTLs for resistance to bacterial blight that will be useful for controlling the disease.

Mapping genes for resistance to bacterial blight (Pseudomonas syringae pv. pisi) in pea and identification of genes involved in resistance by DeepsuperSAGE transcriptome profiling

Bacterial blight caused by Pseudomonas syringae pv. pisi is an important disease of pea (Pisum sativum L.). Knowledge about the genes or mechanisms acting against this pathogen is scarce. A genetic mapping study of the resistance was performed using a recombinant inbred line mapping population generated by crossing the susceptible cultivar Cheyenne to the resistant line ZP0104. Resistance to race 2 was a dominant monogenic trait mapped at 109.4 cM on LGVII between AB114 and AB122 simple sequence repeat markers. It is assumed to be the previously Ppi2 based on its location. Resistance to races 4 and 8 behaved also as dominant monogenic traits and presumably due to a single gene conferring resistance to both races. It was mapped on LGIII at 11.2 cM of the AD57 microsatellite marker. This gene has been named Ppi8 and it is proposed as a new resistance gene. Ppi8 and Ppi2 are associated to the pea consensus map for the first time. To identify genes related to resistance and susceptibility, a DeepSuperSAGE genome-wide transcription profiling approach was conducted producing 45,261 different pea unitags. A set of 651 unitags were differently represented in the susceptible versus the resistant response with a significance of P 4. These putative differentially expressed set includes genes previously related to responses to biotic stresses (pathogenesis-related or related to disease resistance responses), abiotic stresses or of unknown function, among other.

Registration of RTx430/Gaigaoliang Sorghum [Sorghum bicolor (L.) Moench] Recombinant Inbred Line Mapping Population

Sorghum [Sorghum bicolor (L.) Moench.] recombinant inbred line (RIL) mapping population RTx430 × Gaigaoliang (Reg. No. MP‐2, NSL 515993 MAP) was developed at the Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, USDA‐ARS, Lubbock, TX, and released in 2011 via the Germplasm Resources Information Network (GRIN). This population was developed to map early‐season field germinability, seedling vigor, and other important agronomic traits in sorghum and to serve as a long‐term genetic resource. The population is composed of 171 F7 RILs developed by single seed descent method and was evaluated at two locations for field emergence and seedling vigor at Lubbock and New Deal, TX, under early‐season planting (1 April) and under controlled conditions at 12°C. The genotype data for this population consist of 141 simple sequence repeat markers and 2922 single nucleotide polymorphism obtained through genotype‐by‐sequencing technology. Ten quantitative trait loci were detected for early‐season field germination and were used to identify early‐season cold‐tolerant recombinant inbreds with nonpigmented testa that can be used as pollinators in breeding programs.

Field-Based High-Throughput Plant Phenotyping Reveals the Temporal Patterns of Quantitative Trait Loci Associated with Stress-Responsive Traits in Cotton.

The application of high-throughput plant phenotyping (HTPP) to continuously study plant populations under relevant growing conditions creates the possibility to more efficiently dissect the genetic basis of dynamic adaptive traits. Toward this end, we employed a field-based HTPP system that deployed sets of sensors to simultaneously measure canopy temperature, reflectance, and height on a cotton (Gossypium hirsutum L.) recombinant inbred line mapping population. The evaluation trials were conducted under well-watered and water-limited conditions in a replicated field experiment at a hot, arid location in central Arizona, with trait measurements taken at different times on multiple days across 2010–2012. Canopy temperature, normalized difference vegetation index (NDVI), height, and leaf area index (LAI) displayed moderate-to-high broad-sense heritabilities, as well as varied interactions among genotypes with water regime and time of day. Distinct temporal patterns of quantitative trait loci (QTL) expression were mostly observed for canopy temperature and NDVI, and varied across plant developmental stages. In addition, the strength of correlation between HTPP canopy traits and agronomic traits, such as lint yield, displayed a time-dependent relationship. We also found that the genomic position of some QTL controlling HTPP canopy traits were shared with those of QTL identified for agronomic and physiological traits. This work demonstrates the novel use of a field-based HTPP system to study the genetic basis of stress-adaptive traits in cotton, and these results have the potential to facilitate the development of stress-resilient cotton cultivars.

Quantitative trait loci associated with natural diversity in water-use efficiency and response to soil drying in Brachypodium distachyon

All plants must optimize their growth with finite resources. Water use efficiency (WUE) measures the relationship between biomass acquisition and transpired water. In the present study, we performed two experiments to understand the genetic basis of WUE and other parameters of plant-water interaction under control and water-limited conditions. Our study used two inbred natural accessions of Brachypodium distachyon, a model grass species with close phylogenetic affinity to temperate forage and cereal crops. First, we identify the soil water content which causes a reduction in leaf relative water content and an increase in WUE. Second, we present results from a large phenotyping experiment utilizing a recombinant inbred line mapping population derived from these same two natural accessions. We identify QTLs associated with environmentally-insensitive genetic variation in WUE, including a pair of epistatically interacting loci. We also identify QTLs associated with constitutive differences in biomass and a QTL describing an environmentally-sensitive difference in leaf carbon content. Finally, we present a new linkage map for this mapping population based on new SNP markers as well as updated genomic positions for previously described markers. Our studies provide an initial characterization of plant-water relations in B. distachyon and identify candidate genomic regions involved in WUE.

Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea.

Identification of potential genes/alleles governing complex seed-protein content (SPC) is essential in marker-assisted breeding for quality trait improvement of chickpea. Henceforth, the present study utilized an integrated genomics-assisted breeding strategy encompassing trait association analysis, selective genotyping in traditional bi-parental mapping population and differential expression profiling for the first-time to understand the complex genetic architecture of quantitative SPC trait in chickpea. For GWAS (genome-wide association study), high-throughput genotyping information of 16376 genome-based SNPs (single nucleotide polymorphism) discovered from a structured population of 336 sequenced desi and kabuli accessions [with 150–200 kb LD (linkage disequilibrium) decay] was utilized. This led to identification of seven most effective genomic loci (genes) associated [10–20% with 41% combined PVE (phenotypic variation explained)] with SPC trait in chickpea. Regardless of the diverse desi and kabuli genetic backgrounds, a comparable level of association potential of the identified seven genomic loci with SPC trait was observed. Five SPC-associated genes were validated successfully in parental accessions and homozygous individuals of an intra-specific desi RIL (recombinant inbred line) mapping population (ICC 12299 × ICC 4958) by selective genotyping. The seed-specific expression, including differential up-regulation (>four fold) of six SPC-associated genes particularly in accessions, parents and homozygous individuals of the aforementioned mapping population with a high level of contrasting SPC (21–22%) was evident. Collectively, the integrated genomic approach delineated diverse naturally occurring novel functional SNP allelic variants in six potential candidate genes regulating SPC trait in chickpea. Of these, a non-synonymous SNP allele-carrying zinc finger transcription factor gene exhibiting strong association with SPC trait was found to be the most promising in chickpea. The informative functionally relevant molecular tags scaled-down essentially have potential to accelerate marker-assisted genetic improvement by developing nutritionally rich chickpea cultivars with enhanced SPC.

QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.)

The linkage map for the recombinant inbred line (RIL) mapping population derived from late leaf spot (LLS) and rust disease susceptible (TAG 24) and resistant (GPBD 4) varieties of peanut was improved by adding 139 new SSR and transposable element (TE) markers. The improved map now has 289 mapped loci with a total map distance of 1730.8 cM and average inter-marker distance of 6.0 cM across 20 linkage groups. Quantitative trait loci (QTL) analysis using improved genetic map with 289 markers and comprehensive phenotypic data for LLS and rust from 11 seasons could identify a region on linkage group AhXV (B03 linkage group of B genome) which contributed significantly towards LLS and rust resistance. Of the five QTL mapped in this region, three showed high phenotypic variance explained (PVE) for both LLS and rust, and two QTL showed high PVE for only rust. The QTL flanked by GM2009-IPAHM103 had very high PVE of 44.5 % and 53.7 %, respectively for LLS and rust response. Another genomic region on AhXII (B10 linkage group of B genome) contained a QTL flanked by GM1839-GM1009 which had a PVE of 14.1–35.2 % for LLS resistance. A new QTL with marker interval GM1989-AhTE0839 on AhV (A05 linkage group of A genome) showed a PVE of 10.2 % for rust resistance. The new markers, AhTE0498 and AhTE0928 linked to rust resistance were validated using another RIL population of TG 26 × GPBD 4. The marker AhTE0498 showed 49.3–52.3 % PVE, indicating a strong marker validation in the new population. The improved map, QTL and markers for LLS and rust resistance reported in this study will be of immense utility in peanut molecular breeding.

Novel QTL for Stripe Rust Resistance on Chromosomes 4A and 6B in Soft White Winter Wheat Cultivars

Stripe rust (caused by Puccinia striiformis f. sp. tritici) of wheat (Triticum aestivum) is a devastating disease in temperate regions when susceptible varieties are grown and environmental conditions sustain high disease pressures. With frequent and severe outbreaks, disease resistance is a key tool for controlling stripe rust on wheat. The goal of this research was to identify quantitative trait loci (QTL) involved in stripe rust resistance from the important US Pacific Northwest soft white winter wheat varieties “Eltan” and “Finch”. An F2:5 recombinant inbred line (RIL) mapping population of 151 individuals derived from the Finch × Eltan cross was developed through single seed descent. A linkage map comprising 683 unique single nucleotide polymorphism (SNP) loci and 70 SSR markers were used to develop 22 linkage groups consisting of 16 of the 21 chromosomes. Stripe rust data were collected on the RILs during the summers of 2012 to 2014. QTL analysis identified two genomic regions on chromosomes 4A (QYrel.wak-4A) and 6B (QYrfi.wak-6B) associated with resistance from Eltan and Finch, respectively. The results of the QTL analysis showed that QYrel.wak-4A and QYrfi.wak-6B reduced infection type and disease severity. Based upon both molecular and phenotypic differences, QYrel.wak-4A is a novel QTL for adult plant resistance (APR) to stripe rust.

Morphoagronomic characterization and genetic diversity of a common bean RIL mapping population derived from the cross Rudá x AND 277.

Recombinant inbred lines (RILs) are a valuable resource for building genetic linkage maps. The presence of genetic variability in the RILs is essential for detecting associations between molecular markers and loci controlling agronomic traits of interest. The main goal of this study was to quantify the genetic diversity of a common bean RIL population derived from a cross between Rudá (Mesoamerican gene pool) and AND 277 (Andean gene pool). This population was developed by the single seed descent method from 500 F2 plants until the F10 generation. Seven quantitative traits were evaluated in the field in 393 RILs, the parental lines, and five control cultivars. The plants were grown using a randomized block design with additional controls and three replicates. Significant differences were observed among the RILs for all evaluated traits (P < 0.01). A comparison of the RILs and parental lines showed significant differences (P < 0.01) for the number of days to flowering (DFL) and to harvest (DH), productivity (PROD) and mass of 100 beans (M100); however, there were no significant differences for plant architecture, degree of seed flatness, or seed shape. These results indicate the occurrence of additive x additive epistatic interactions for DFL, DH, PROD, and M100. The 393 RILs were shown to fall into 10 clusters using Tocher's method. This RIL population clearly contained genetic variability for the evaluated traits, and this variability will be crucial for future studies involving genetic mapping and quantitative trait locus identification and analysis.

Early anthesis and delayed but fast leaf senescence contribute to individual grain dry matter and water accumulation in wheat

The physiological process of how anthesis time and leaf senescence patterns affect individual grain weight of wheat has only been partially elucidated. In this study, a recombinant inbred line mapping population of bread wheat (Triticum aestivum L. ‘Forno’) and its relative spelt (Triticum spelta L. ‘Oberkulmer’), contrasting for phasic development and leaf senescence kinetics, was used to understand the physiological and genetic relationships among anthesis time, leaf senescence, grain filling processes, and individual grain weight. Phenotypic measurements were taken in the field over two growing seasons. The results showed that earlier anthesis and delayed leaf senescence were associated with larger grains. Furthermore, early anthesis and delayed but fast leaf senescence promoted grain filling rate (but shortened its duration), grain water absorption rate and maximum grain water content, while individual grain dry matter and water accumulation displayed strong relationships with individual grain weight. A total of 118 significant quantitative trait loci (QTL) were identified in this mapping population, including six QTL for anthesis dates, 24 for flag leaf senescence, 69 for grain filling traits, and 19 for individual grain weight. Frequent QTL coincidences between these traits were observed on chromosomes 2A, 3B, 4A, 4DL, 5A, 5B, 5DL and 7B. Analysis of allelic effects confirmed the above physiological relationships. Therefore, anthesis time and leaf senescence affect individual grain weight at least partly through their effects on individual grain dry matter and water accumulation, resulting from pleiotropy or tight gene linkages. Slightly early anthesis, and delayed but fast leaf senescence, can be used to maximize individual grain weight and yield potential in wheat.

Spelt as a Genetic Resource for Yield Component Improvement in Bread Wheat

ABSTRACTNovel germplasm resources are required to broaden the genetic diversity of bread wheat (Triticum aestivum L.) for further yield improvement. In this study, the usefulness of spelt (T. spelta L.) as a genetic resource to improve yield components of bread wheat was determined. A recombinant inbred line mapping population of bread wheat Forno and spelt Oberkulmer was used to quantify the yield components. Subsequently, quantitative trait loci (QTL) for yield components, together with grain threshability traits, were identified. Oberkulmer had larger grains (in 2012 season), more fertile tillers, higher biomass, longer and laxer spikes than Forno. Quantitative trait locus analysis revealed six alleles for low threshability and two for tenacious glumes from the spelt, and the Q gene had major effects. Furthermore, 40 favorable alleles for yield components were detected from Oberkulmer, and 83% of them were independent of those for low threshability and tenacious glumes. Therefore, spelt is a useful genetic resource for yield component improvement of bread wheat, while maintaining the free‐threshing habit. In addition, most of QTL for grain number components were coincident with those for grain weight. Allelic analysis of the coincident QTL showed that increased grain number was associated with decreased grain weight, which explained their negative phenotypic relationships.

Genetic analysis of germinating ability and seedling vigor under cold stress in US weedy rice

Low temperature stress is a major constraint for rice production in temperate and high altitude areas of the world. Delayed germination coupled with reduced seedling vigor hinders crop establishment and crop growth resulting in reduced rice productivity. Mapping of the chromosomal regions controlling cold tolerance will accelerate marker-assisted breeding of cold tolerant rice varieties. A recombinant inbred line mapping population involving a US weedy rice accession ‘PSRR-1’ and a rice cultivar ‘Bengal’ was evaluated for germinating ability and seedling vigor under low temperature (13 °C) and optimum temperature (28 °C). ‘PSRR-1’ performed better than ‘Bengal’ under cold stress. Forty-nine QTL distributed over ten chromosomes were identified for 11 traits. The number of QTL varied from one to nine with phenotypic variability of each QTL ranging from 3.5 to 12.7 %. For 18 QTL, ‘Bengal’ alleles were desirable, whereas ‘PSRR-1’ allele improved germination and seedling vigor under cold stress in 31 QTL. Three major QTL were observed for coleoptile length and seedling shoot length. The QTL were clustered in six chromosomal regions. The congruency of QTL cluster on chromosome 11 with earlier studies suggests a potential target for cloning cold tolerance genes at germination and seedling stages. This study demonstrated that weedy rice can be a valuable donor for desirable alleles to improve germination and seedling stage cold tolerance in rice.

Registration of the OhW (Oh43×W64A) Maize Recombinant Inbred Mapping Population

The Oh43×W64A (OhW) maize (Zea mays L.) mapping population (MP‐3, NSL 511549 MAP) consists of 255 recombinant inbred lines (RILs). This mapping population was constructed from a cross between inbred lines Oh43 (Ames 19288) and W64A (PI 587152). Our primary goal was to develop a mapping population segregating for a large number of important agronomic traits using a cross of lines that formed a heterotic hybrid used in the northern Corn Belt. Genetic markers were scored using genotyping‐by‐sequencing technology, and a high‐density genetic map was constructed using the single nucleotide polymorphism data. A wide range of phenotypic diversity among individuals, and transgressive segregation, was observed for all traits measured. The registration of this RIL mapping population provides geneticists and breeders with a highly diverse set of lines in combination with a dense genetic map that can be utilized to identify quantitative trait loci at high mapping resolution.

Discovery and mapping of genomic regions governing economically important traits of Basmati rice.

BackgroundBasmati rice, originated in the foothills of Himalayas, commands a premium price in the domestic and international markets on account of its unique quality traits. The complex genetic nature of unique traits of Basmati as well as tedious screening methodologies involved in quality testing have been serious constraints to breeding quality Basmati. In the present study, we made an attempt to identify the genomic regions governing unique traits of Basmati rice.ResultsA total of 34 Quantitative Trait Loci (QTLs) for 16 economically important traits of Basmati rice were identified employing F2, F3 and Recombinant Inbred Line (RIL) mapping populations derived from a cross between Basmati370 (traditional Basmati) and Jaya (semi-dwarf rice). Out of which, 12 QTLs contributing to more than 15 % phenotypic variance were identified and considered as major effect QTLs. Four major effect QTLs coincide with the already known genes viz., sd1, GS3, alk1 and fgr governing plant height, grain size, alkali spreading value and aroma, respectively. For the remaining major QTLs, candidate genes were predicted as auxin response factor for filled grains, soluble starch synthase 3 for chalkiness and VQ domain containing protein for grain breadth and grain weight QTLs, based on the presence of non-synonymous single nucleotide polymorphism (SNPs) that were identified by comparing Basmati genome sequence with that of Nipponbare.ConclusionsTo the best of our knowledge, the current study is the first attempt ever made to carry out genome-wide mapping for the dissection of the genetic basis of economically important traits of Basmati rice. The promising QTLs controlling important traits in Basmati rice, identified in this study, can be used as candidates for future marker-assisted breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0575-5) contains supplementary material, which is available to authorized users.

Carpel size, grain filling, and morphology determine individual grain weight in wheat.

Individual grain weight is a major yield component in wheat. To provide a comprehensive understanding of grain weight determination, the carpel size at anthesis, grain dry matter accumulation, grain water uptake and loss, grain morphological expansion, and final grain weight at different positions within spikelets were investigated in a recombinant inbred line mapping population of bread wheat (Triticum aestivum L.)×spelt (Triticum spelta L.). Carpel size, grain dry matter and water accumulation, and grain dimensions interacted strongly with each other. Furthermore, larger carpels, a faster grain filling rate, earlier and longer grain filling, more grain water, faster grain water absorption and loss rates, and larger grain dimensions were associated with higher grain weight. Frequent quantitative trait locus (QTL) coincidences between these traits were observed, particularly those on chromosomes 2A, 3B, 4A, 5A, 5DL, and 7B, each of which harboured 16-49 QTLs associated with >12 traits. Analysis of the allelic effects of coincident QTLs confirmed their physiological relationships, indicating that the complex but orderly grain filling processes result mainly from pleiotropy or the tight linkages of functionally related genes. After grain filling, distal grains within spikelets were smaller than basal grains, primarily due to later grain filling and a slower initial grain filling rate, followed by synchronous maturation among different grains. Distal grain weight was improved by increased assimilate availability from anthesis. These findings provide deeper insight into grain weight determination in wheat, and the high level of QTL coincidences allows simultaneous improvement of multiple grain filling traits in breeding.

Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis.

Delayed transition from the vegetative stage to the reproductive stage of development and increased plant height have been shown to increase biomass productivity in grasses. The goal of this project was to detect quantitative trait loci using extremes from a large synthetic population, as well as a related recombinant inbred line mapping population for these two traits. Ten thousand individuals from a B73 × Mo17 noninbred population intermated for 14 generations (IBM Syn14) were grown at a density of approximately 16,500 plants ha−1. Flowering time and plant height were measured within this population. DNA was pooled from the 46 most extreme individuals from each distributional tail for each of the traits measured and used in bulk segregant analysis (BSA) sequencing. Allelic divergence at each of the ∼1.1 million SNP loci was estimated as the difference in allele frequencies between the selected extremes. Additionally, 224 intermated B73 × Mo17 recombinant inbred lines were concomitantly grown at a similar density adjacent to the large synthetic population and were assessed for flowering time and plant height. Using the BSA sequencing method, 14 and 13 genomic regions were identified for flowering time and plant height, respectively. Linkage mapping with the RIL population identified eight and three regions for flowering time and plant height, respectively. Of the regions identified, three colocalized between the two populations for flowering time and two colocalized for plant height. This study demonstrates the utility of using BSA sequencing for the dissection of complex quantitative traits important for production of lignocellulosic ethanol.