Parental Polymorphism Research Articles

Inheritance and molecular mapping of the genomic regions governing seedviability in soybean (Glycine max. L. Merr.)

Loos of seed viability in soybean (Glycine max L. Merrill, 2n=40) during ambient storage from harvest to the next planting season is a significant barrier for the production of high-quality seeds. The present study includes the inheritance and molecular mapping of the loci linked to seed viability in soybean. For this, five high viable genotypes (>90% germination after one year of storage) viz. EC-1023, EC-105790, G2651, UPSL34, UPSL736 and three poorly viable genotype (<70% germination after one year of storage) viz. MACS-565, PK1243, VLS61 were hybridized in all possible combination. Obtained F1 were advanced separately. Cross EC1023 x VLS61 and their derived F2:3 seeds, were exposed to 72 hours of accelerated ageing (AA) at 41°C and 100% RH, followed by a germination. After AA test, germination % of EC1023 and VL5-61 were 40 and 14, respectively, whereas range of F2:3 seeds were 4.16 to 71.42 %. The seed viability is governed by polygenes or quantitative trait loci (QTL), as evidenced by the continuous distribution of germination % of F2:3 seeds. Parental polymorphism was studied with 506 SSR markers indicated it to 20.35% whereas distribution of the polymorphism was not uniform across the chromosomes; Chr. 15 had 46.15% polymorphism as against 15.78% on Chr. 3 and 4. Through inclusive composite interval mapping 8 QTL for seed viability on Chr. 6, 7, 8, 10, 13 and 17, respectively, were mapped. Two of the eight QTLs appear to be major QTLs, as their PVE percent is greater than 10% and other seems as minor ones. Previously reported markers linked to seed viability were also validated in the parental genotypes, with only Satt538 being able to differentiate the five good and three poor storing genotypes. The genetics of seed viability, as well as the QTLs and markers found in this study, will pave the way for molecular breeding to generate genotypes with improved seed viability.

Evaluation for Parental Polymorphism and Identification of Microsatellites Linked to Drought Tolerance in Rice (Oryza sativa L.)

Aims: To identify the ready-to-use polymorphic microsatellite markers associated with drought tolerance for marker-assisted backcross breeding through a polymorphism survey between Jyothi and Chuvannamodan rice varieties.
 Place and Duration of Study: Centre for plant biotechnology and molecular biology, Thrissur, Kerala, India, during January to May 2023.
 Methodology: The genomic DNA of Jyothi and Chuvannamodan was isolated by following CTAB (Cetyltrimethyl Ammonium Bromide) method with modification. Isolated DNA from both varieties was subjected to PCR amplification using 208 Simple Sequence Repeats (SSRs) primer pairs distributed in 12 chromosomes. The amplified PCR products were electrophoresed in 3% agarose gel and separated fragments were visualized and documented in the Gel Documentation System. Different allele sizes produced by the same SSRs primers between two varieties are identified as polymorphic markers. Polymorphism per-cent was calculated, and frequency distribution and chromosome distribution of polymorphic markers were analyzed.
 Results: A total of 208 SSR primers were surveyed for the parental polymorphism. Out of which, 85 SSR primers exhibited clear polymorphism between Jyothi and Chuvannamodan and the remaining 123 were monomorphic primers. The amplicon size ranged from 83bp (RM430) to 495bp (RM18919) among the different primers. The survey revealed maximum parental polymorphism on chromosome 4 (69.23%), followed by chromosome 5 (64.28%), and minimum polymorphism on chromosome 8 (21.73%). The average per cent of polymorphism between the parents was 40.86%. Among the 85 polymorphic markers, 66 had dinucleotide repeats, 17 had trinucleotide repeats, and 1 had tetranucleotide repeats.
 Markers with dinucleotide repeats showed higher level of polymorphism. A group of 28 polymorphic markers were identified to be linked with traits including root-related traits, grain yield, leaf rolling and leaf drying under drought conditions.
 Conclusion: The polymorphic markers identified in the present study form the basis for tagging drought-tolerant QTLs/genes, fine mapping of those genes, and subsequently in marker-assisted breeding programs. The polymorphic markers linked with the QTLs for grain yield under drought can be pyramided in Jyothi through marker-assisted backcross breeding.

Bulk Segregant Analysis for the Identification of Shoot Fly Resistance Linked Molecular Marker in Sorghum [Sorghum bicolor (L.) Moench]

Sorghum (Sorghum bicolor (L.) Moench) is one of the most important crops in the semi-arid regions of the world. One of the important biotic constraints to sorghum production in India is the shoot fly which attacks sorghum at the seedling stage. The study was undertaken during 2021–22 at the Centre for Millets Research, Sardarkrushinagar Dantiwada Agricultural University, Deesa, Gujarat, India to assess linked molecular markers for sorghum shoot fly resistance using the bulk segregant analysis (BSA) method with simple sequence repeat (SSR) marker from developed F2 mapping population with two genetically diverse parental lines, SWARNA (susceptible to shoot fly) and IS 18551 (resistant to shoot fly). Sixty-five SSRs primers pair were used for the parental polymorphism survey using two contrasting parents to detect the primers exhibiting polymorphism. Eight out of sixty-five primers showed polymorphism (12.30%) between two contrasting parental lines in sorghum. Two out of eight polymorphic SSRs primer pairs i.e., Xtxp 67 and Xgap 88 were found polymorphic between resistance and susceptibility in parents and bulks and thus reported to be putatively linked with shoot fly. Bulk segregant analysis (BSA) was extended to identify the traits controlled by minor genes with additive effects, which increased the power and efficiency of this molecular technique to construct genetic map in the sorghum crop improvement program. The identified SSRs markers i.e., Xtxp 67 and Xgap 88 might be useful to screen resistance for shoot fly infestation in future sorghum improvement program.

Identification of new molecular markers for low glucosinolates in Indian mustard (Brassica juncea L. Czern & Coss.)

The study was carried out to identify molecular markers linked to low glucosinolates in Brassica juncea usingrecombinant inbred lines developed from cross between Pusa Mustard 21 × EC597325. Parental polymorphism studies with 594 SSR markers, revealed 62 informative markers. The bulk segregant analysis (BSA) revealed fourmicrosatellite markers differentiating both the parental lines and the high and low glucosinolates bulks, henceputatively linked to the genomic regions controlling low glucosinolates.

Construction of a Tomato (Solanum lycopersicum L.) Introgression Line Population and Mapping of Major Agronomic Quantitative Trait Loci

Tomato as a fresh fruit has a large market share in China, but few new materials have been developed for such cultivar breeding in recent years. This study aims to create innovative breeding materials for fresh fruit tomatoes with consistent genetic backgrounds and take advantage of beneficial genes from wild germplasm resources. An introgression line (IL) population was constructed using freshly cultivated tomato S. lycopersicum 1052 and wild tomato S. pennellii LA0716 through hybridization and five consecutive backcrossings, with molecular marker-assisted selection techniques during seedling stages. A total of 447 cleaved amplified polymorphic sequences (CAPS) and 525 simple sequence repeat (SSR) markers were used to screen polymorphic markers among the two parental lines, resulting in 216 polymorphic CAPS and 236 polymorphic SSR markers, with 46.5% parental polymorphism. Then, 200 molecular markers uniformly distributed over the entire genome were further selected, and 107 ILs were finally obtained from 541 BC5 candidate plants. The physical distance between adjacent markers was 6.3~10.0 cm, with an average interval of 7.29 cm, and the IL population constructed covered the whole genome of S. pennillii LA0716, with an average introgression segment of 31.5 cm. Moreover, phenotype data of major agronomic traits in BC5 progeny after selfing two times, were analyzed for quantitative trait locus (QTL) mapping, and a total of 11 QTLs distributed on 6 chromosomes were identified, including 3 QTLs regulating plant height, 1 QTL regulating leaf size, 1 QTL regulating fruit color, 4 QTLs regulating fruit weight, and 2 QTLs regulating soluble solids content in ripening fruits. The IL population constructed in this study provided good materials for fresh fruit tomato breeding with improved yield and quality in the future.

Parental Polymorphism Survey for Identifying Genes/QTLs for BPH Resistance in Assam Land Race 10-3

The current research was taken up at Institute of Biotechnology (IBT), PJTSAU, Hyderabad Telangana, India in kharif from August to November, 2021 to access the parental polymorphism between 10-3 and Telangana Sona. 10-3, an Assam landrace, is a bold grain rice variety with high BPH resistance to biotype-4. Whereas, Telangana Sona (RNR 15048) is a short and slender grain variety of rice that is popular among farmers and consumers across Telangana and other Indian states due to its high yield and low glycemic index. Despite being blast resistant, Telangana Sona is susceptible to the insect pest Brown Plant hopper (BPH) Nilaparvata lugens (Stål). The present study aimed to characterize the parental polymorphism between 10–3 and Telangana sona to facilitate mapping of genetic loci linked with BPH resistance in the 10–3 and to optimize the retention of favourable alleles from Telangana sona during marker assisted backcross breeding. Eight hundred and sixteen highly variable Simple Sequence Repeats (SSRs) including thirty-five BPH linked markers covering 12 chromosomes were used to assess DNA polymorphism between 10-3 and Telangana Sona. Out of 816 markers screened, 97 (11.89%) were found to be polymorphic between 10–3 and Telangana Sona of which, 82 were genomic SSRs and 15 were BPH linked markers. Chromosome 6 exhibited highest polymorphism percentage with a value of 30%, indicating that this chromosome is useful in studying parental variation and lowest polymorphism percentage found on chromosome 5 (3.49%). These 97 polymorphic markers will help in construction of linkage map for identifying QTLs linked with BPH resistance and for marker assisted backcrossing breeding in Telangana Sona.

Parental Polymorphism between Samba Mahsuri and False Smut Tolerant Landraces using SSR and InDel Markers

In the present study, 868 SSR and 475 InDel markers were selected to study parental polymorphism of two different crosses between recipient parent Samba Mahsuri and false smut donor linesIC379047 and IC334233 at ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad. Out of 1343 markers used for parental polymorphism, 100 markers were polymorphic between parental lines Samba Mahsuri and landrace IC379047 and the total polymorphism percentage recorded was 7.44%. Ninety-nine markers exhibited polymorphism between parental lines Samba Mahsuri and IC334233 and 7.37% of total polymorphism percentage was recorded between the parents. The identified polymorphic markers could be further used for QTL mapping studies in false smut resistance.

Parental polymorphism survey using rice microsatellite markers between VGD 1 and ADT 55 for marker-assisted backcross breeding program

Parental polymorphism survey using rice microsatellite markers between VGD 1 and ADT 55 for marker-assisted backcross breeding program

Gene Validation for Brown Plant Hopper Resistance in Rice Varieties Using SSR Markers

The Brown Plant Hopper (BPH), Nilaparvata lugens (Homoptera: Delphacidae) is one of the most destructive insect pests causing significant yield loss in most of the rice cultivars of Asia. Marker-assisted backcrossing is used to introgress the genes for BPH resistance in which the selection of donor parents to confer durable resistance and validation of the presence of genes is a prerequisite. Jyothi the most popular, widely cultivated rice variety in Kerala is screened along with four parental lines viz., PTB33 (Variety released from RARS, Pattambi), IRRI introgressed lines- IR65482-7-216-1-2, IR7103-121-15-B, and a breeding line RP2068-13-5-8 for validating the presence of genes Bph3, BPH18, Bph20, and Bph21 using SSR markers. Parental polymorphism was shown for markers specific to Bph3, BPH18, and Bph20. Besides this, cluster analysis using the UPGMA method produced 4 clusters. The variety ‘PTB33’ was obtained in a separate cluster which can be attributed to its resistant character against BPH and can be considered as a potential donor. The IRRI introgressed lines- IR65482-7-216-1-2, IR7103-121-15-B, and the breeding line RP2068-13-5-8 can also be well utilized as donors by proper standardized BPH screening tests for confirming the phenotypic expression of BPH resistance.

QTL Mapping of Leaf-Related Traits Using a High-Density Bin Map in Brassica rapa

The species Brassica rapa includes enormous leafy vegetables with extreme leaf morphological diversity. Leaf traits such as size, shape, weight, and ratio of the leaf blade to the petiole contribute to yield, appearance, and desirability to consumers. These leaf-related traits are controlled by quantitative trait loci (QTLs). The construction of high-density bin maps using low-coverage sequencing is a powerful method for QTL fine-mapping and gene identification. In this study, we performed whole-genome re-sequencing of Wutacai ‘Zhongbaye’ and Chinese cabbage ‘HN53’ and 150 F2 individuals to construct a high-density bin map for QTL mapping of 11 leaf-related traits. The parental lines and F2 population were re-sequenced at 10x and 1x coverage, respectively. A map containing 565 bin markers was constructed based on parental single-nucleotide polymorphisms and a modified sliding window approach. The total map length was 944.6 cM and the average distance of the bins was 1.65 cM. In total, 60 significant QTLs controlling 11 leaf-related traits were detected. We further identified candidate genes responsible for these complex leaf-related traits. These findings suggest that this cost-effective bin-mapping approach is capable of rapid identification of QTLs and candidate genes, and will thus facilitate the dissection of the underlying molecular basis of leaf morphological variations and accelerate the improvement of B. rapa vegetable breeding.

Morpho-biochemical characterization of a RIL population for seed parameters and identification of candidate genes regulating seed size trait in lentil (Lens culinaris Medik.).

The seed size and shape in lentil (Lens culinaris Medik.) are important quality traits as these influences the milled grain yield, cooking time, and market class of the grains. Linkage analysis was done for seed size in a RIL (F5:6) population derived by crossing L830 (20.9 g/1000 seeds) with L4602 (42.13 g/1000 seeds) which consisted of 188 lines (15.0 to 40.5 g/1000 seeds). Parental polymorphism survey using 394 SSRs identified 31 polymorphic primers, which were used for the bulked segregant analysis (BSA). Marker PBALC449 differentiated the parents and small seed size bulk only, whereas large seeded bulk or the individual plants constituting the large-seeded bulk could not be differentiated. Single plant analysis identified only six recombinant and 13 heterozygotes, of 93 small-seeded RILs (<24.0 g/1000 seed). This clearly showed that the small seed size trait is very strongly regulated by the locus near PBLAC449; whereas, large seed size trait seems governed by more than one locus. The PCR amplified products from the PBLAC449 marker (149bp from L4602 and 131bp from L830) were cloned, sequenced and BLAST searched using the lentil reference genome and was found amplified from chromosome 03. Afterward, the nearby region on chromosome 3 was searched, and a few candidate genes like ubiquitin carboxyl-terminal hydrolase, E3 ubiquitin ligase, TIFY-like protein, and hexosyltransferase having a role in seed size determination were identified. Validation study in another RIL mapping population which is differing for seed size, showed a number of SNPs and InDels among these genes when studied using whole genome resequencing (WGRS) approach. Biochemical parameters like cellulose, lignin, and xylose content showed no significant differences between parents and the extreme RILs, at maturity. Various seed morphological traits like area, length, width, compactness, volume, perimeter, etc., when measured using VideometerLab 4.0 showed significant differences for the parents and RILs. The results have ultimately helped in better understanding the region regulating the seed size trait in genomically less explored crops like lentils.

Genome-wide identification and characterization of parthenocarpic fruit set-related gene homologs in cucumber (Cucumis sativus L.)

Cucumber (Cucumis sativus L.), a major horticultural crop, in the family Cucurbitaceae is grown and consumed globally. Parthenocarpy is an ideal trait for many fruit and vegetables which produces seedless fruit desired by consumers. The seedlessness occurs when fruit develops without fertilization which can be either natural or induced. So far, a limited number of genes regulating parthenocarpic fruit set have been reported in several fruit or vegetable crops, most of which are involved in hormone biosynthesis or signalling. Although parthenocarpic cucumber has been widely used in commercial production for a long time; its genetic basis is not well understood. In this study, we retrieved thirty five parthenocarpy fruit-set related genes (PRGs) from bibliomic data in various plants. Thirty-five PRG homologs were identified in the cucumber genome via homology-based search. An in silico analysis was performed on phylogenetic tree, exon–intron structure, cis-regulatory elements in the promoter region, and conserved domains of their deduced proteins, which provided insights into the genetic make-up of parthenocarpy-related genes in cucumber. Simple sequence repeat (SSR) sequences were mined in these PRGs, and 31 SSR markers were designed. SSR genotyping identified three SSRs in two polymorphic genes. Quantitative real-time PCR of selected genes was conducted in five cucumber lines with varying degrees of parthenocarpic fruit set capacities, which revealed possible association of their expression with parthenocarpy. The results revealed that homologs CsWD40 and CsPIN-4 could be considered potential genes for determination of parthenocarpy as these genes showed parental polymorphism and differential gene expression in case of parthenocarpic and non-parthenocarpic parents.

Screening microsatellite markers for establishing parental polymorphism in Indian rice (Oryza sativa L.)

The experiment was conducted to investigate the parental diversity along the rice genome and to understand and screen out the SSR markers-indicated polymorphism between two indica rice (Oryza sativa L.) cultivars. Namely K343, the most well-liked rice variety in the hill zone of the Jammu Region, and RML22, a rice line created at IRRI, Philippines. The study is to select polymorphic markers (Simple Sequence Repeat- SSR) associated with hill ecologies rice cultivars and additional research projects like gene pyramiding and background selection to recover the recurrent parent genome (RPG) in blast gene introgression in elite lines. 450 SSR markers, evenly distributed throughout the rice genome, were used to assess the parental polymorphism between these genotypes. Of these two cultivars, 51 markers (11.33%) showed polymorphism with bands in different spectrums throughout the genome. The study has been used to Marker Assisted Backcross (MAB) breeding to integrate rice blast resistance genes in the parental genotype. The pool of polymorphic markers has the potential to use in similar studies and work, with a high probability of polymorphism for the cultivars of hill ecologies, and thus increase the chance of selection of probability in marker selection.

Association of parental HLA-G polymorphisms with soluble HLA-G expressions and their roles on recurrent implantation failure: A systematic review and meta-analysis.

HLA-G plays a central role in immune tolerance at the maternal-fetal interface. The HLA-G gene is characterized by low allelic polymorphism and restricted tissue expression compared with classical HLA genes. HLA-G polymorphism is associated with HLA-G expression and linked to pregnancy complications. However, the association of parental HLA-G polymorphisms with soluble HLA-G (sHLA-G) expression and their roles in recurrent implantation failure (RIF) is unclear. The study aims to systematically review the association of HLA-G polymorphisms with RIF, the association of sHLA-G expression with RIF, and the association of HLA-G polymorphisms with sHLA-G expressions in patients attending in-vitro fertilization (IVF) treatment. Studies that evaluated the association of HLA-G polymorphisms with RIF, the association between sHLA-G expression with RIF, and the association between HLA-G polymorphisms with sHLA-G expressions in patients attending IVF treatment were included. Meta-analysis was performed by random-effect models. Sensitivity analysis was performed by excluding one study each time. Subgroup analysis was performed based on ethnicity. HLA-G 14bp ins variant is associated with a lower expression of sHLA-G in seminal or blood plasma of couples attending IVF treatment. The maternal HLA-G*010101 and paternal HLA-G*010102 alleles are associated with RIF risk compared to other alleles. However, single maternal HLA-G 14bp ins/del polymorphism, HLA-G -725 C>G/T polymorphism, or circulating sHLA-G concentration was not significantly associated with RIF in the general population. HLA-G 14bp ins/ins homozygous genotype or ins variant was associated with a higher risk of RIF in the Caucasian population. Specific HLA-G alleles or HLA-G polymorphisms are associated with sHLA-G expression in couples attending IVF treatment. Several HLA-G polymorphisms may be related to RIF, considering different ethnic backgrounds. A combined genetic effect should be considered in future studies to confirm the association of HLA-G polymorphisms and sHLA-G expressions in relation to RIF.

Identification of F1 Hybrid Progenies in Mango Based on Fluorescent SSR Markers

Mango (Mangifera indica L.) belongs to the genus Mangifera and family Anacardiaceae, and is an important tropical fruits. Artificial cross breeding (hand pollination) is an important method for breeding new mango cultivars. It is easy to produce false hybrids in the process of artificial pollination breeding. Therefore, it is necessary to establish rapid and accurate molecular detection methods to identify the authenticity of hybrids. Mango ‘Jinhuang’ and ‘Renong No.1′ and 65 individual plants of their F1 hybrids were used as experimental materials, eight SSRs (simple sequence repeats) primer pairs with polymorphism in parents were used to identify the F1 hybrids by capillary electrophoresis. The results showed that PCR product size (bp) for eight primers ranged from 108 bp (ES55) to 176 bp (ES63) in 65 samples. A total of 62 true hybrids were identified from 65 hybrid progenies, and the true hybrid rate was 95.38%. A total of 18 alleles were amplified by eight SSRs, seven SSR loci showed binary segregations, whereas only one SSR locus ES83 showing ab:ac:bb:bc segregation fitted to the expected segregation ratio of 1:1:1:1. The value of expected heterozygosity (He), ranged from 0.34 to 0.62, whereas the value of observed heterozygosity ranged from 0.44 to 0.81. Chi-square test showed that eight SSR loci were in accordance with Mendel’s segregation law. The results of cluster analysis showed that the parents and 62 true hybrids could be classified into two categories at 0.58: the first category contained 27 offspring, clustered with ‘Jinhuang’ and showed a maternal genetic tendency. The second category contained 35 offspring, clustered with ‘Renong No.1′ and showed a partial paternal genetic tendency. DNA fingerprint of hybrids from ‘Jinhuang’ × ‘Renong No.1′ cross were constructed using eight SSR primers for variety protection.

Impact of parental chromosomal polymorphisms on the incidence of congenital anomalies and perinatal complications in a cohort of newborns conceived after ICSI + PGT-A.

BackgroundTo assess the association between chromosomal polymorphisms (CPM) with congenital anomalies and perinatal complications in a cohort of newborns from couples undergoing intracytoplasmic sperm injection (ICSI), trophectoderm biopsy, and preimplantation genetic testing for aneuploidy (PGT-A).MethodsA retrospective cohort of singletons conceived after ICSI, trophectoderm biopsy, and PGT-A cycles performed at IVIRMA clinics in Spain over 4 years was involved in the study. Newborns were classified according to the parental karyotype analysis: Group I: non-carriers, Group II: CPM carriers. Couples with chromosomal anomalies and instances when both partners were CPM carriers were excluded from the study. The groups were compared for several perinatal complications.ResultsThere was a significant decrease in the number of NB with complications in the carrier group compared to the non-carriers (19.7% vs 31.9%, p = 0.0406). There were no statistical differences among the two groups regarding congenital anomalies, preterm birth, alterations in birth length and weight, cranial perimeter, Apgar test score, or sex ratio (p > 0.05).ConclusionsChromosomal polymorphisms appear to have no adverse effects on congenital anomalies or perinatal complications on newborns from ICSI + PGT-A cycles.

Parental Polymorphism Survey for Evaluation and Selection of Contrasting Parents for Drought Tolerance in Rice (Oryza sativa L.) by Using SSR Markers

Aim: This study aims to find the informative polymorphic Microsatellite (SSR) markers for drought tolerance between the recipient parent (Pratishya) and donor parent (CR Dhan 801) of rice. The drought tolerant QTLs (qDTY1.1, qDTY2.1, and qDTY3.1) from the donor parent were subsequently introgressed into the popular variety Pratikshya via marker-assisted backcross breeding.&#x0D; Place and Duration of Study: The parental polymorphism study was conducted at Molecular Drought Breeding Laboratory, Department of Genetics and Plant Breeding and Central Laboratory, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi; and at Crop Improvement Division, ICAR-NRRI, Cuttack during Rabi 2018-19.&#x0D; Methodology: The parents used for the study were Pratikshya (recurrent parent) and CR Dhan 801 (donor parent). The leaf samples were collected from 20-25 days old seedlings which were used for parental polymorphism survey after DNA extraction. The genomic DNA isolation was done by using CTAB method. A set of 510 SSR markers covering all the 12 chromosomes of rice were used for parental polymorphism survey in the present study. The standard protocol of polymerase chain reaction (PCR) and agarose gel electrophoresis was used. The DNA fragments were documented using gel documentation system. The graphical representation of marker data was obtained with GGT 2.0 software.&#x0D; Results: Out of 510, total 108 SSR primer pairs exhibited polymorphism between recipient parent (Pratikshya) and donor parent (CR Dhan 801) and remaining 392 SSR primers were monomorphic. The highest percentage of parental polymorphism was observed on chromosome 2 (26.53%) and 3 (26.46%) followed by chromosome 1 (23.08%); and least on chromosome number 10 (14.71%). The average per cent of polymorphism on all the 12 chromosomes were 21.28%. Out of 108 polymorphic markers obtained from screening of 510 SSRs, 69 contained dinucleotide repeats, 32 showed trinucleotide repeats and 5 were having tetranucleotide repeats.&#x0D; Conclusion: The screening of markers by parental polymorphism in rice cultivars gives the basis for tagging of the target gene, fine mapping of the gene on the rice chromosome, and subsequent application in Marker Assisted Selection (MAS) programmes. The polymorphic markers identified in this study were be used for genotyping the entire mapping population and for the introgression of the QTLs/genes linked with grain yield during the reproductive stage of drought.

Construction of Genetic Linkage Map and Mapping QTL Specific to Leaf Anthocyanin Colouration in Mapping Population 'Allahabad Safeda' × 'Purple Guava (Local)' of Guava (Psidium guajava L.).

In the present investigation, F1 hybrids were developed in guava (Psidium guajava L.) by crossing high leaf-anthocyanin reflective-index (ARI1) content cultivars purple guava (local) ‘PG’, ‘CISH G-1’ and low leaf-ARI1 content cultivar Seedless ‘SL’ with Allahabad Safeda ‘AS’. On the basis of phenotypic observations, high ARI1 content was observed in the cross ‘AS’ × ‘PG’ (0.214). Further, an SSR-markers-based genetic linkage map was developed from a mapping population of 238 F1 individuals derived from cross ‘AS’ × ‘PG’. The linkage map comprised 11 linkage groups (LGs), spanning 1601.7 cM with an average marker interval distance of 29.61 cM between adjacent markers. Five anthocyanin-content related gene-specific markers from apple were tested for parental polymorphism in the genotypes ‘AS’ and ‘PG’. Subsequently, a marker, viz., ‘MdMYB10F1′, revealed a strong association with leaf anthocyanin content in the guava mapping population. QTL (qARI-6-1) on LG6 explains much of the variation (PVE = 11.51% with LOD = 4.67) in levels of leaf anthocyanin colouration. This is the first report of amplification/utilization of apple anthocyanin-related genes in guava. The genotypic data generated from the genetic map can be further exploited in future for the enrichment of linkage maps and for identification of complex quantitative trait loci (QTLs) governing economically important fruit quality traits in guava.

IDENTIFICATION OF LOW GRAIN SHATTERING QTLS IN RICE USING BACKCROSS INBRED LINES OF MTU1010

Rice is an important food crop in Asia and is predominant in India. Rice crop is affected by biotic or abiotic stresses which culminate in yield loss. Grain shattering is physiological problem among the several stresses in rice. Some rice varieties which are improved through breeding still have problems like grain shattering. The mega variety MTU 1010 has several desirable traits but having high grain shattering has been a major drawback. Therefore identification of QTLs for low grain shattering is important for improving MTU 1010 with marker assisted breeding programmes. Eighty four backcross inbred lines in BC2F8 generation were developed from the cross MTU1010/JGL17004. The parental polymorphism survey was carried out with 626 SSR markers. Out of these, 88 markers were polymorphic between the parents. The population was subjected to genotyping with the eighty eight polymorphic markers. The genotyping data was used in QTL ICImapping Version 4.2 to generate a linkage map which covered 2381cM. The IM and ICIM analysis detected 29 and 22 QTLs respectively at a LOD threshold of 2.0. The epistatic analysis detected 453 epistatic QTLs. Four novel QTLs viz., qSh-2-1, qSh-2-2, qSh-3-1 and qSh-10-1 for shattering were detected in both ICIM and IM. These four QTLs were also co-localized with 24 epistatic QTLs. Among the four QTLs identified in the present study, qSh-3-1 on chromosome 3 is far away from the QTLs reported earlier while, the QTL qSh-2-2 might be nearer to the gene (OsGRF4) for moderate grain shattering identified in earlier studies. But till date, none of the QTLs were identified for low grain shattering on chromosome 10. The current study also identified some major QTLs viz., qPHt-3-1 , qDFF-6-1, qPL-8-1, qUFG-2-1, qSF-2-1 and qTW-6-1 with high phenotypic variance. The BILs with low grain shattering can be utilized for further confirmation studies and the regions with QTLs for low grain shattering can be analyzed more precisely. So that they can be introgressed into the varieties with high grain shattering.

Marker assisted introgression of semi-dwarfing (sd1) gene in Katarni rice (Oryza sativa L.) landrace

Abstract ‘Katarni Rice’ is a fine quality scented rice landrace of Bihar, India and has tremendous export potential and commercial value. This is a preferred rice in the state due to its flavour, palatability and popcorn like essence before and after cooking. But its area has been shrunken drastically in recent years due to its low yielding (25–30 Q/ha) ability caused due tall and week stature and lodging tendency at maturity. To overcome this problem, marker assisted introgression of semi-dwarfing (sd1) gene from semi-dwarf and high yielding rice varieties Rajendra Sweta and BPT5204 was attempted. Parental polymorphism was obtained through 109 SSR markers. The gene specific markers for fragrance and semi-dwarfing genes were used in the segregants to track their transfer. Recombinant selection was done for the donor genome segments flanking to the target gene i.e., sd1 followed by background selection through genome wide polymorphic SSR markers. More than 90% recurrent parent genome recovery was observed and the selected plants showed a reduction of plant height and flowering time in comparison to Katarni in the successive backcross generation along with the retention of aroma. The identified lines can be evaluated further in multilocation trials to release it as a sustainable high yielding aromatic genotype.