Polymorphic SSR Markers Research Articles

Towards Defining Heterotic Gene Pools in Pearl Millet [Pennisetum glaucum (L.) R. Br.

Pearl millet is a climate resilient crop and one of the most widely grown millets worldwide. Heterotic hybrid development is one of the principal breeding objectives in pearl millet. In a maiden attempt to identify heterotic groups for grain yield, a total of 343 hybrid parental [maintainer (B-) and restorer (R-)] lines were genotyped with 88 polymorphic SSR markers. The SSRs generated a total of 532 alleles with a mean value of 6.05 alleles per locus, mean gene diversity of 0.55, and an average PIC of 0.50. Out of 532 alleles, 443 (83.27%) alleles were contributed by B-lines with a mean of 5.03 alleles per locus. R-lines contributed 476 alleles (89.47%) with a mean of 5.41, while 441 (82.89%) alleles were shared commonly between B- and R-lines. The gene diversity was higher among R-lines (0.55) compared to B-lines (0.49). The unweighted neighbor-joining tree based on simple matching dissimilarity matrix obtained from SSR data clearly differentiated B- lines into 10 sub-clusters (B1 through B10), and R- lines into 11 sub-clusters (R1 through R11). A total of 99 hybrids (generated by crossing representative 9 B- and 11 R- lines) along with checks were evaluated in the hybrid trial. The 20 parents were evaluated in the line trial. Both the trials were evaluated in three environments. Based on per se performance, high sca effects and standard heterosis, F1s generated from crosses between representatives of groups B10R5, B3R5, B3R6, B4UD, B5R11, B2R4, and B9R9 had high specific combining ability for grain yield compared to rest of the crosses. These groups may represent putative heterotic gene pools in pearl millet.

A new gene Bph33(t) conferring resistance to brown planthopper (BPH), Nilaparvata lugens (Stål) in rice line RP2068-18-3-5

The rice brown planthopper (BPH) Nilaparvata lugens (Stal) is one of the major pests of rice across Asia. Host-plant resistance is the most ecologically acceptable means to manage this pest. A rice breeding line RP2068-18-3-5 (RP2068) derived from the land race Velluthacheera is reported to be resistant to BPH populations across India. We identified a new R gene [Bph33(t)] in this line using advanced generation RILs derived from TN1 × RP2068 cross through phenotyping at two locations and linkage analysis with 99 polymorphic SSR markers. QTL analysis through IciMapping identified at least two major QTL on chromosome 1 influencing seedling damage score in seed box screening, honey dew excretion by adults and nymphal survival. Since no BPH R gene has been reported on chromosome 1, we designate this locus as a new gene Bph33(t) which accounted for over 20% of phenotypic variance. Scanning the region for candidate gene suggested two likely candidates a leucine rich repeat (LRR) gene and a heat shock protein (HSP) coding gene. Expression profiling of the two genes in the two contrasting parents and RILs showed induction of the HSP gene (LOC_Os01g42190.1) at 6 h after infestation while LRR gene did not show such induction. It is likely that the HSP represented Bph33(t).

Species delimitation and conservation genetics of the Canarian endemic Bethencourtia (Asteraceae).

Bethencourtia Choisy ex Link is an endemic genus of the Canary Islands and comprises three species. Bethencourtia hermosae and Bethencourtia rupicola are restricted to La Gomera, while Bethencourtia palmensis is present in Tenerife and La Palma. Despite the morphological differences previously found between the species, there are still taxonomic incongruities in the group, with evident consequences for its monitoring and conservation. The objectives of this study were to define the species differentiation, perform population genetic analysis and propose conservation strategies for Bethencourtia. To achieve these objectives, we characterized 10 polymorphic SSR markers. Eleven natural populations (276 individuals) were analyzed (three for B. hermosae, five for B. rupicola and three for B. palmensis). The results obtained by AMOVA, PCoA and Bayesian analysis on STRUCTURE confirmed the evidence of well-structured groups corresponding to the three species. At the intra-specific level, B. hermosae and B. rupicola did not show a clear population structure, while B. palmensis was aggregated according to island of origin. This is consistent with self-incompatibility in the group and high gene flow within species. Overall, the genetic diversity of the three species was low, with expected heterozygosity values of 0.302 (B. hermosae), 0.382 (B. rupicola) and 0.454 (B. palmensis). Recent bottleneck events and a low number of individuals per population are probably the causes of the low genetic diversity. We consider that they are naturally rare species associated with specific habitats. The results given in this article will provide useful information to assist in conservation genetics programs for this endemic genus.

SSR-based association mapping of fiber quality in upland cotton using an eight-way MAGIC population.

The quality of fiber is significant in the upland cotton industry. As complex quantitative traits, fiber quality traits are worth studying at a genetic level. To investigate the genetic architecture of fiber quality traits, we conducted an association analysis using a multi-parent advanced generation inter-cross (MAGIC) population developed from eight parents and comprised of 960 lines. The reliable phenotypic data for six major fiber traits of the MAGIC population were collected from five environments in three locations. Phenotypic analysis showed that the MAGIC lines have a wider variation amplitude and coefficient than the founders. A total of 284 polymorphic SSR markers among eight parents screened from a high-density genetic map were used to genotype the MAGIC population. The MAGIC population showed abundant genetic variation and fast linkage disequilibrium (LD) decay (0.76cM, r2 > 0.1), which revealed the advantages of high efficiency and power in QTL exploration. Association mapping via a mixed linear model identified 52 significant loci associated with six fiber quality traits; 14 of them were mapped in reported QTL regions with fiber-related or other agronomic traits. Nine markers demonstrated the pleiotropism that controls more than two fiber traits. Furthermore, two SSR markers, BNL1231 and BNL3452, were authenticated as hotspots that were mapped with multi-traits. In addition, we provided candidate regions and screened six candidate genes for identified loci according to the LD decay distance. Our results provide valuable QTL for further genetic mapping and will facilitate marker-based breeding for fiber quality in cotton.

Heterotic response of genomic regions derived from Oryza rufipogon and O. nivara in improving grain morphology and quality of indica rice (Oryza sativa L.)

Limited backcrossing was followed to introgress useful variability, needed for improving grain morphology and milling traits, from wild Oryza species into two indica cultivars PR114 and Pusa44.These alien introgressions lines (ILs), having similar grain quality parameters to the recurrent parent, were used for developing rice hybrids to assess the effect of these introgressions in the heterozygous state and to assess their grain quality parameters, as most of the hybrids commercialized in the tropics have inferior grain quality. These ILs and their recurrent parents, possessing fertility restoration ability for wide abortive cytoplasm, were crossed with CMS line PMS 17A to generate introgressions line hybrids (ILHs). Hybrids developed from recurrent parents were used as a check to compare the performance of ILHs. Based on yield and phenotypic acceptability, six ILHs having enriched genome of O. rufipogon and O. nivara were selected and analyzed for grain quality traits. All six hybrids observed significant improvement in milled rice recovery (up to 10%), head rice recovery (up to 25%) over ILs and check hybrids. Introgressions were analyzed using polymorphic SSR markers. The majority of O. rufipogon and O.nivara alleles identified in the study seems to be effective across recipient genotypes and could be used effectively in quality breeding programs.

QTL mapping for traits at reproductive stage drought stress in rice using single marker analysis

Drought is the major abiotic constraint leading to very high yield reduction in both rain-fed upland and lowland areas worldwide. Reproductive stage is the most sensitive to water deficiency as compared to vegetative stage of rice. In this present investigation, association between phenotype and genotype was carried out for the drought mapping population of CR143-2-2/Krishnahamsa to detect QTLs through single marker analysis (SMA). A total of 21 polymorphic SSR markers were detected through bulked segeregant analysis approach. QTL mapping was performed through ICIM v4.0 software. Only phenotypic trait, days to 50% flowering (DFF) at reproductive stage stress showed association with chromosome 1 and 6. A significant higher peak was obtained in RM3825 marker linked in chromosome 1 detected to be a novel QTL, qDFF1.1 controlling flowering under drought stress. The other QTL on chromosome 6 is validated in this mapping population which controls flowering under terminal drought stress.

Simple Sequence Repeat Marker based Mapping of gene for Yellow Mosaic Virus (YMV) Resistance in Soybean (Glycine max L. Merill.)

Yellow Mosaic Virus (YMV) is a prominent pathogen that has been posing threat to soybean production in the country. About 30–50% of yield loss due to YMV is reported every year. The disease has also been reported in the North East India. Effective environment friendly chemical and cultural practices are not possible for this viral disease. Genetic resistance, therefore, needs to be deployed for the management of YMV. A set of 60 soybean accessions were tested for YMV resistance in North East Indiaas a preliminary attempt for initiation of breeding programme in soybean for resistance to YMV. Mapping population were developed by crossing identified genotypes both resistant and susceptible. A set of 40 polymorphic SSR markers were identified to show polymorphism with respect to resistance to YMV. Bulk Segregant Analysis was performed in the F2 plants using these markers. The gene was mapped using MAPMAKER 3.0. Marker survey indicated close association of the markers Satt174, Satt599 and Satt200 with resistance to YMV. The gene responsible for YMV, Gene Ymv-IV, was located on short arm of chromosome No. 5, and both the markers are located on either side of the gene at distance of 6.9cM and 8.7cM, respectively. The markers identified can be used for further polymorphism studies in new genotypes. The markers associated with the YMV resistance may be valuable in molecular breeding programme for YMV resistance in soybean.

Physiological and molecular characterisation for high temperature stress in Lens culinaris.

In the present study, 11 lentil (Lens culinaris Medik) genotypes including heat tolerant and heat sensitive genotypes identified after a screening of 334 accessions of lentil for traits imparting heat tolerance, were characterised based on physiological traits and molecular markers. Results showed a higher reduction in pollen viability among sensitive genotypes (up to 52.3%) compared with tolerant genotypes (up to 32.4%) at 43°C. Higher photosynthetic electron transport rate was observed among heat tolerant genotypes and two heat tolerant lentil genotypes, IG 4258 (0.43) and IG 3330 (0.38) were having highest Fv/Fm values. However, membrane stability was significantly higher in only one heat tolerant genotype, ILL 10712, indicating that different mechanisms are involved to control heat tolerance in lentil. The molecular characterisation of lentil genotypes with 70 polymorphic SSR and genic markers resulted into distinct clusters in accordance with their heat stress tolerance. A functional marker ISM11257 (intron spanning marker) amplifying an allele of 205bp in size was present only among heat tolerant genotypes, and could be further used in a breeding program to identify heat tolerant lentil genotypes. The findings of this study will contribute to the development of heat tolerant lentil cultivars.

Integrating marker-assisted background analysis with foreground selection for pyramiding bacterial blight resistance genes into Basmati rice

Bacterial leaf blight (BB), caused by the bacterium Xanthomonas oryzae pv. Oryzae (Xoo), is the major constraint amongst rice diseases in India. CSR-30 is a very popular high-yielding, salt-tolerant Basmati variety widely grown in Haryana, India, but highly susceptible to BB. In the present study, we have successfully introgressed three BB resistance genes (Xa21, xa13 and xa5) from BB-resistant donor variety IRBB-60 into the BB-susceptible Basmati variety CSR-30 through marker-assisted selection (MAS) exercised with stringent phenotypic selection without compromising the Basmati traits. Background analysis using 131 polymorphic SSR markers revealed that recurrent parent genome (RPG) recovery ranged up to 97.1% among 15 BC3F1 three-gene-pyramided genotypes. Based on agronomic evaluation, BB reaction, aroma, percentage recovery of RPG, and grain quality evaluation, four genotypes, viz., IC-R28, IC-R68, IC-R32, and IC-R42, were found promising and advanced to BC3F2 generation.

Characterization of some bread wheat genotypes using molecular markers for drought tolerance.

Because of its wide geographical adaptation and importance in human nutrition, wheat is one of the most important crops in the world. However, wheat yield has reduced due to drought stress posing threat to sustainability and world food security in agricultural production. The first stage of drought tolerant variety breeding occurs on the molecular and biochemical characterization and classification of wheat genotypes. The aim of the present study is characterization of widely grown bread wheat cultivars and breeding lines for drought tolerance so as to be adapted to different regions in Turkey. The genotypes were screened with molecular markers for the presence of QTLs mapped to different chromosomes. Results of the molecular studies identified and detected 15 polymorphic SSR markers which gave the clearest PCR bands among the control genotypes. At the end of the research, bread wheat genotypes which were classified for tolerance or sensitivity to drought and the genetic similarity within control varieties were determined by molecular markers. According to SSR based dendrogram, two main groups were obtained for drought tolerance. At end of the molecular screening with SSR primers, genetic similarity coefficients were obtained that ranged from 0.14 to 0.71. The ones numbered 8 and 11 were the closest genotypes to drought tolerant cultivar Gerek 79 and the furthest genotypes from this cultivar were number 16 and to drought sensitive cultivar Sultan 95. The genotypes as drought tolerance due to their SSR markers scores are expected to provide useful information for drought related molecular breeding studies.

Association of functional markers with flowering time in lentil.

In the present study, a diverse panel of 96 accessions of lentil germplasm was used to study flowering time over environments and to identify simple sequence repeat markers associated with flowering time through association mapping. The study showed high broad sense heritability estimate (h 2 bs=0.93) for flowering time in lentil. Screening of 534 SSR markers resulted in an identification of 75 SSR polymorphic markers (13.9%) across studied genotypes. These markers amplified 266 loci and generated 697 alleles ranging from two to 16 alleles per locus. Model-based cluster analysis used for the determination of population structure resulted in the identification of two distinct subpopulations. Distribution of flowering time was ranged from 40 to 70 days in subpopulation I and from 54 to 69 days in subpopulation II and did not skew either late or early flowering time within a subpopulation. No admixture was observed within the subpopulations. Use of the most accepted maximum likelihood model (P3D mixed linear model with optimum compression) of MTA analysis showed significant association of 26 SSR markers with flowering time at <0.05 probability. The percent of phenotypic explained by each associated marker with flowering time ranged from 2.1 to 21.8% and identified QTLs for flowering time explaining high phenotypic variation across the environments (10.7-21.8%) or in a particular environment (10.2-21.4%). In the present study, 13 EST-SSR showed significant association with flowering time and explained large phenotypic variation (2.3-21.8%) compared to genomic SSR markers (2.1-10.2%). Hence, these markers can be used as functional markers in the lentil breeding program to develop short duration cultivars.

Study of Transferability of Rubus Microsatellite Markers to Hybrid Boysenberry

Boysenberry, a Rubus hybrid between loganberry and a trailing blackberry, possesses distinctive polyphenol compounds, which have demonstrated positive biological effects on human health. Several new boysenberry genotypes have recently been developed from mutation breeding technology. In this study, a total of 103 SSR markers developed from expressed sequence tag (EST) and genomic libraries in blackberry and red raspberry were tested for cross-amplifications in 10 boysenberry genotypes. All primer pairs successfully produced amplification products, ranging from 1 to 4 loci per primer. Eleven polymorphic SSR markers (RH_MEa0007aB01, RH_MEa12cE03, RH_MEa14bF07, RH_MEa15aD04, RH_MEa13cF08, ERubLR_SQ01_N03, ERubLR_ SQ053_H01, ERubLR_SQ191_A05, RubfruitG7, Rubusr43a, and RiM019) were detected among boysenberry genotypes, while polymorphic loci were not detected in 92 markers. Polymorphism information content (PIC) and genetic diversity (GD) values ranged from 0.160 to 0.580 and from 180 to 0.640, with average values of 0.359 and 0.407, respectively, in the 11 polymorphic markers. According to a cluster analysis, all the mutant boysenberry genotypes can be classified into one category. Although the level of genetic diversity revealed by SSR markers in 10 boysenberry genotypes was low, these SSR markers will be useful for future genetic diversity, cultivar identification, QTL mapping, and gene cloning studies in boysenberry.

Keragaman Genetik antar Klon Kopi Robusta Lokal Pagar Alam berdasarkan Analisis Marka SSR

&lt;em&gt;Robusta coffee (&lt;/em&gt;Coffea canephora &lt;em&gt;var. robusta) is the most extensive developed in Indonesia, including Pagar Alam, South Sumatra. In the last few decades, many farmers in Pagar Alam conducted clonal selection and rehabilitation of Robusta coffee trees that generated indigenous clonal populations. This pattern in the long period can damage important alleles and reduce the genetic diversity of indigenous Robusta coffee in farmland. The research aimed to know the genetic diversity among indigenous Robusta coffee clones developed in Pagar Alam based on SSR markers. The study was conducted at Molecular Biology Laboratory, Cereals Research Institute, Maros, from February to April 2017. Molecular characterization of 19 indigenous Robusta coffee clones was conducted using 33 polymorphic SSR markers. The resulting binary data was then analyzed using PowerMarker program to determine polymorphism value (PIC), number and diversity of alleles, and heterozygosity values. The results showed that 33 polymorphic SSR loci produced 134 alleles with an average of 4.06 alleles/locus, whereas PIC values &lt;/em&gt;&lt;em&gt;ranged from 0.09&lt;/em&gt;–&lt;em&gt;0.77 with an average of 0.48. Of the 33 SSR loci, 19 loci (57.58%) exhibited very informative PIC value (&amp;gt; 0.55). Dendrogram generated using NTSYS program divided 19 indigenous Robusta coffee clones into 4 clusters at 0.53 similarity coefficient. KPA41clone was separated in its own cluster, potentially crossed with other clones. Based on genetic distance values &amp;gt;0.55, could arrange 14 combinations of interclonal crosses that potentially increase the genetic variability of indigenous Robusta coffee from Pagar Alam.&lt;/em&gt;

Phenotypic Screening and Molecular Characterization of 10 Rice (Oryza sativa) Landraces for Cold Tolerance

Phenotypic screening of existing 10 familiar landraces performed at germination and seedling stages and their molecular characterization were conducted at Bangladesh Institute of Nuclear Agricultural (BINA) during the period of December 2014 to May 2015 to screen out better cold tolerant genotypes among 10 landraces where one susceptible, two moderately tolerant and two tolerant BRRI released varieties were used as check genotypes. The present study evaluated several parameters at the germination stage after 7 days of germination and at the seedling stage after 28 days of seedling growth for phenotypic screening. Modified hydroponic method was used at the seedling stage and the temperature treatments were maintained artificially at 15°C and 25°C respectively. Polymorphic microsatellite or SSR markers were selected for molecular characterization showing that attributes were positively regulated due to cold stress in BRRIdhan 36, LR 114- Badiabona and LR 54- Tor Balam. The findings of genetic diversity analysis for landraces LR 114- Badiabona and LR 54- Tor Balam appeared to resemble to that of tolerant genotype BRRIdhan 36. Based on phenotypic screening and UPGMA dendrogram study, landraces LR 114- Badiabona and LR 54- Tor Balam appeared superior as genetic material. Better cold tolerant rice variety may be developed from further breeding process.J. Environ. Sci. &amp; Natural Resources, 10(1): 85-91 2017

Development of SSR Markers and Their Use in Studying Genetic Diversity and Population of Finger Millet (Eleusine coracana L. Gaertn.)

Finger millet (Eleusine coracana L. Gaertn.) is an important cereal crop in eastern Africa and southern India with excellent grain storage capacity and the unique ability to thrive in extreme environmental conditions. In this study, we analyzed the genetic diversity and population structure of finger millet using 12 developed microsatellites. By sequencing 815 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in finger millet accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 76 finger millet accessions in Asia, Africa, and unknown origins. The number of alleles ranged from 2 to 9, with an average of 3.3 alleles. The mean values of observed heterozygosity and expected heterozygosity were 0.27 and 0.35, respectively. The average polymorphism information content was 0.301 in all 76 finger millet accessions. AMOVA analysis showed that the percentage of molecular variance among the populations was 1%, that among individuals was 5%, and that within individuals was 94%. In STRUCTURE analysis, the 76 finger millet accessions were divided into two subpopulations which had an admixture of alleles. There was a correspondence among PCoA, AMOVA, and population structure. This study may form the basis for a finger millet breeding and improvement program.

Genetic structure of putative heterotic populations of alfalfa

AbstractSemi‐hybrids between genetically distant alfalfa (Medicago sativa subsp. sativa) populations may display heterosis whose extent is affected by the structure of genetic diversity across populations. This study aimed to assess the genetic diversity across three putative heterotic populations, one Italian, one Egyptian and one of semi‐erect germplasm from Eastern Europe, Canada and Spanish Mielga (EECM population). Each population was bred from ten parents after various selection cycles. Fifteen genotypes per population were characterized by 20 polymorphic SSR markers. The among‐population variance was over eightfold smaller than the average within‐population variance (2.05 vs. 17.24) and accounted for 10.6% of the total variation. G’ST = .090 across markers indicated modest population differentiation. Various diversity measures, multidimensional scaling, and cluster analysis of the genetic structure indicated that the Italian population was more distant from the EECM population than the Egyptian one. The EECM and Egyptian populations were the most distant geographically and genetically. EECM displayed widest intrapopulation variation, accordingly to its constitutive geographical diversity. In conclusion, this study indicates modest genetic differentiation between alfalfa populations even for geographically distant germplasm.

Molecular characterization and genetic diversity of different genotypes of Oryza sativa and Oryza glaberrima

Background: Availability of related rice species is critical for rice breeding and improvement. Two distinct species of domesticated rice exist in the genus Oryza: Oryza sativa (Asian rice) and Oryza glaberrima (African rice). New rice for Africa (NERICA) is derived from interspecific crosses between these two species. Molecular profiling of these germplasms is important for both genetics and breeding studies. We used 30 polymorphic SSR markers to assess the genetic diversity and molecular fingerprints of 53 rice genotypes of O. sativa , O. glaberrima , and NERICA. Results: In total, 180 alleles were detected. Average polymorphism information content and Shannon's information index were 0.638 and 1.390, respectively. Population structure and neighbor-joining phylogenetic tree revealed that 53 genotypes grouped into three distinct subpopulations conforming to the original three groups, except three varieties (IR66417, WAB450-4, MZCD74), and that NERICA showed a smaller genetic distance from O. sativa genotypes (0.774) than from O. glaberrima genotypes (0.889). A molecular fingerprint map of the 53 accessions was constructed with a novel encoding method based on the SSR polymorphic alleles. Ten specific SSR markers displayed different allelic profiles between the O. glaberrima and O. sativa genotypes. Conclusions: Genetic diversity studies revealed that 50 rice types were clustered into different subpopulations whereas three genotypes were admixtures. Molecular fingerprinting and 10 specific markers were obtained to identify the 53 rice genotypes. These results can facilitate the potential utilization of sibling species in rice breeding and molecular classification of O. sativa and O. glaberrima germplasms. Normal 0 false false false ES-CL X-NONE X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:Tabla normal; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri,sans-serif; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-bidi-font-family:Times New Roman; mso-bidi-theme-font:minor-bidi; mso-ansi-language:ES-CL;}

Validation of SSR markers linked to oil content in groundnut (Arachis hypogaea L.)

A set of 14 SSR markers that are specific for six QTLs for oil content reported by various authors was selected for validation in the present study. The F4:5 mapping population of the cross ICGV 00440 x ICGV 03128 was used to validate the markers as well as QTLs specific for oil content. Among the selected markers, six markers were polymorphic for the parents ICGV 00440 and ICGV 03128. Among the six polymorphic SSR markers, two markers IPAHM103 and PGS16F10 revealed a strong association for oil content with a PVE of 15.3 and 19.6 respectively in single marker analysis. Validation of QTLs was also performed through composite interval mapping analysis. A QTL with flanking markers IPAHM103 and PM36 could be considered as a potential tool for marker assisted selection of the trait oil content in groundnut.

Enriching an intraspecific genetic map and identifying QTL for fiber quality and yield component traits across multiple environments in Upland cotton (Gossypium hirsutum L.).

Cotton is a significant commercial crop that plays an indispensable role in many domains. Constructing high-density genetic maps and identifying stable quantitative trait locus (QTL) controlling agronomic traits are necessary prerequisites for marker-assisted selection (MAS). A total of 14,899 SSR primer pairs designed from the genome sequence of G. raimondii were screened for polymorphic markers between mapping parents CCRI 35 and Yumian 1, and 712 SSR markers showing polymorphism were used to genotype 180 lines from a (CCRI 35×Yumian 1) recombinant inbred line (RIL) population. Genetic linkage analysis was conducted on 726 loci obtained from the 712 polymorphic SSR markers, along with 1379 SSR loci obtained in our previous study, and a high-density genetic map with 2051 loci was constructed, which spanned 3508.29cM with an average distance of 1.71cM between adjacent markers. Marker orders on the linkage map are highly consistent with the corresponding physical orders on a G. hirsutum genome sequence. Based on fiber quality and yield component trait data collected from six environments, 113 QTLs were identified through two analytical methods. Among these 113 QTLs, 50 were considered stable (detected in multiple environments or for which phenotypic variance explained by additive effect was greater than environment effect), and 18 of these 50 were identified with stability by both methods. These 18 QTLs, including eleven for fiber quality and seven for yield component traits, could be priorities for MAS.

Inheritance and a major quantitative trait locus of seed starch content in mungbean (Vigna radiata (L.) Wilczek)

Mungbean (Vigna radiata) seeds are used for direct consumption by people and are raw material for sprout, starch and noodle industries in Asia. High-yielding mungbean cultivars with high seed starch content are preferred for the starch and noodle industries. At present, there is no report on genetic control of seed starch content in mungbean. The objective of this study were to (i) estimate heritability of the starch content in mungbean and (ii) locate a major quantitative trait locus (QTL) controlling starch content. An F2 population of 123 individuals was developed from the cross V6087AG (high seed starch) × V5020BY (low seed starch). Seeds of F2 and F2:3 populations were determined for seed starch content. Broad-sense heritability estimated for seed starch content in the F2 and F2:3 populations were higher than 80%. Seed starch content showed a relatively high and significant correlation (r = 0.6) with seed weigh in both F2 and F2:3 populations. Bulk segregant analysis using 123 polymorphic SSR markers revealed that only SSR marker CEDG092 on mungbean chromosome 8 associated with the starch content. QTL mapping using CEDG092 and 22 newly developed SSR markers the chromosome confirmed that a major QTL, qSSC8.1, flanked by markers Vr08-SSR113 and Vr08-SSR114 control seed starch content in both F2 and F2:3 populations. qSSC8.1 showed no localization with seed weight QTL and explained about 12.34–13.84% of total variation of the seed starch content in the two populations. Allele(s) from V6087AG at this QTL increased seed starch content. Vr08-SSR113 and Vr08-SSR114 spanned a genome region of about 385 Kbp and there were 21 annotated genes in this region. This genome region can be used as target for fine mapping to identify gene controlling seed starch content in mungbean.