BC1F1 Populations Research Articles

Phenotypic Characterization and Gene Mapping of a Spiral Leaf and Dwarf (sld) Mutant from Tetraploid Common Tobacco (Nicotiana tabacum L.)

Leaf morphology and plant height are two agronomic traits closely related to tobacco (Nicotiana tabacum L.) yield and quality. The study of leaf morphology and plant stature mutants will greatly contribute to the fields of plant architecture breeding and developmental biology. Here, we report the characterization of a spiral leaf and dwarf (sld) mutant identified from an ethylmethane sulfonate (EMS)-induced common tobacco population. The sld mutant displayed the phenotype of wrinkled, spiral, and miniature leaves, with the growth point as the central axis and plant dwarfing with shortened internodes. The inheritance pattern of the sld mutant phenotype was manipulated by a recessive nuclear monogene, which was linked to six tobacco simple sequence repeat (SSR) markers from linkage group 5 via gene mapping. Utilizing an F2 population, the sld mutant gene the sld mutant gene was located between the co-segregated markers PT51778, PT54913, and the marker PT61414, with an equal genetic distance of 0.16 cM. Taking advantage of a BC1F1 population, the markers PT51778, PT54913, the sld gene, and the marker PT61414 demonstrated co-segregation, located between the markers PT40040 and PT60933, respectively, with a genetic distance of 1.37 cM and 6.32 cM, respectively. These findings will be helpful in cloning the sld gene and in the further characterization of the regulatory genes controlling the spiral and dwarfing phenotypes in tobacco.

Marker Assisted Introgression of Saltol QTL into “APMS 6B” to Enhance Salt Tolerance at Seedling Stage of Rice (Oryza sativa L.)

APMS 6B which is highly sensitive to salinity was used as a recurrent parent to introgress Saltol QTL from FL-478. Two gene linked markers viz., RM8094 and RM10793 were used for used to confirm backcross generations for saltol QTL. Two successive backcrosses were attempted to transfer target alleles of Saltol from FL478 into APMS-6B. After backcross progrmme, the BC2F1 plants subjected to foreground selection by using gene specific markers, positive plants for target gene were selected and selfed to raise BC2F2 populations. Twenty BC2F2 plants were identified to be homozygous dominant for Saltol QTL and these BC2F2 lines were also screened in plastic trays using Yoshida solution at the seedling stage. A total of BC2F2 lines were confirmed for the target gene and displayed a high level of salinity tolerance without any symptoms on their leaves, with a score of ‘0’.

Introgression of Stay Green Quantitative Trait Locus (QTLS) into Elite Sorghum Variety by MABC

Sorghum is a major staple food crop for the people in semi-arid areas of Asia. Post-flowering drought is a global constraint of sorghum production. The study aimed to improve stay-green characteristics of GS-23 sorghum variety by transferring stg3A and stg3B QTL`s respectively from donor genotypes K260 and K359w of ICRISAT by using marker assisted backcrossing. The experimental material comprised of six basic generations P1, P2, F1, F2, BC1 and BC2 developed from crossing GS-23 × K260 and GS-23 × K359 were genotyped using a set of 133 SNPs and 79 SSR markers. Whereas, 53 polymorphic SNPs among parents and backcross F1s for stay green trait at maturity were used to track introgression of stay green trait. Similarly,10 SSR markers were found to be polymorphic were used to track introgression of stay green trait i.e., stay green trait QTL`s stg3A and stg3B from donor parent K260 and K359w respectively in GS-23 background across backcross population and to identify plants that were homozygous for the desired allele. In which 02 SNPs SnpSB0039 and SnpSB0093 were identified as polymorphic for both K260 and K359w. Whereas 17 SNPs identified polymorphic for K260 and 34 SNPs for K359w. These SNPs were validated in both F1 and BC1F1 populations of both the crosses. Similarly, out of 10 SSR markers utilized, 02 SSRs were identified polymorphic to K260 and 02 SSRs were identified for K359w. Whereas 06 SSRs were polymorphic to both the parents K260 and K359w. Prominent 02 SSRs viz., Xtxp 141_Fam and Xgap84_Vic found to be more reliable and polymorphic to both the parents. These SSRs were validated in both F1 and BC1F1 populations of both the crosses. The genotypic analysis revealed the presence of favorable alleles in homozygous conditions at markers loci associated with stg3A and stg3B QTL`s in BC populations, suggesting successful introgression of stay green QTLs from the donor parents to the recurrent parent. Therefore, our study demonstrated the utility of marker-assisted backcrossing for drought tolerance improvement of locally adapted sorghum variety.

Mapping the gene of a maize leaf senescence mutant and understanding the senescence pathways by expression analysis.

Narrowing down to a single putative target gene behind a leaf senescence mutant and constructing the regulation network by proteomic method. Leaf senescence mutant is an important resource for exploring molecular mechanism of aging. To dig for potential modulation networks during maize leaf aging process, we delimited the gene responsible for a premature leaf senescence mutant els5 to a 1.1Mb interval in the B73 reference genome using a BC1F1 population with 40,000 plants, and analyzed the leaf proteomics of the mutant and its near-isogenic wild type line. A total of 1355 differentially accumulated proteins (DAP) were mainly enriched in regulation pathways such as "photosynthesis", "ribosome", and "porphyrin and chlorophyll metabolism" by the KEGG pathway analysis. The interaction networks constructed by incorporation of transcriptome data showed that ZmELS5 likely repaired several key factors in the photosynthesis system. The putative candidate proteins for els5 were proposed based on DAPs in the fined QTL mapping interval. These results provide fundamental basis for cloning and functional research of the els5 gene, and new insights into the molecular mechanism of leaf senescence in maize.

Identification of salt stress-tolerant candidate genes in the BC2F2 population at the seedling stages of G. hirsutum and G. darwinii using NGS-based bulked segregant analysis.

Salinity is a major threat to the yield and productivity of cotton seedlings. In the present study, we developed a BC2F2 population of cotton plants from Gossypium darwinii (5-7) and Gossypium hirsutum (CCRI 12-4) salt-susceptible parents to identify salt-resistant candidate genes. The Illumina HiSeq™ strategy was used with bulked segregant analysis. Salt-resistant and salt-susceptible DNA bulks were pooled by using 30 plants from a BC2F2 population. Next-generation sequencing (NGS) technology was used for the sequencing of parents and both bulks. Four significant genomic regions were identified: the first genomic region was located on chromosome 18 (1.86 Mb), the second and third genomic regions were on chromosome 25 (1.06 Mb and 1.94 Mb, respectively), and the fourth was on chromosome 8 (1.41 Mb). The reads of bulk1 and bulk2 were aligned to the G. darwinii and G. hirsutum genomes, respectively, leading to the identification of 20,664,007 single-nucleotide polymorphisms (SNPs) and insertions/deletions (indels). After the screening, 6,573 polymorphic markers were obtained after filtration of the candidate regions. The SNP indices in resistant and susceptible bulks and Δ(SNP-index) values of resistant and susceptible bulks were measured. Based on the higher Δ(SNP-index) value, six effective polymorphic SNPs were selected in a different chromosome. Six effective SNPs were linked to five candidate genes in four genomic regions. Further validation of these five candidate genes was carried out using reverse transcription-quantitative polymerase chain reaction (RT-qPCR), resulting in an expression profile that showed two highly upregulated genes in the salt-tolerant species G. darwinii, i.e., Gohir.D05G367800 and Gohir.D12G239100; however, the opposite was shown in G. hirsutum, for which all genes, except one, showed partial expression. The results indicated that Gohir.D05G367800 and Gohir.D12G239100 may be salt-tolerant genes. We are confident that this study could be helpful for the cloning, transformation, and development of salt-resistant cotton varieties.

A stable quantitative trait locus on chromosome A10 improves the oil content of a backbone parent in Brassica napus L.

One of the most important breeding goals for rapeseed (Brassica napus L.) is improving the oil content (OC) to increase edible or industrial oil quality. Using backbone parents as research materials to excavate OC genetic loci is not only helpful in enhancing the understanding of the genetic basis of OC in rapeseed but also offers a promising approach to improve backbone parents. In this study, a doubled haploid population constructed using the backbone parent 19514 A (with low OC) and the inbred line ZY50 (with high OC) were investigated in eight environments. A total of 30 quantitative trait loci (QTLs) were identified, among which qOC.A10 was detected in six environments. Local QTL scanning for the BC4F2 population showed that qOC.A10 accounted for 22.77% of the phenotypic variance and 0.97% of the additive effect. Further, we improved the parent 19514 A on qOC.A10 by marker-assisted selection, and the background response rate of the improved line A10–19514A reached 97.5%. The phenotypic identification results showed that the OC of A10–19514A and its hybrid significantly increased compared with that of the control, with no negative effects on other agronomic traits. Transcriptome analysis and sequence difference analysis facilitated the prediction of potential functional genes of qOC.A10. This study increases the knowledge regarding the genetic foundation of OC in rapeseed. Furthermore, it identified and confirmed a stable QTL that can be detected in various studies and possesses practical breeding significance.

Breeding evaluation and precise mapping of Fhb8 for Fusarium head blight resistance in wheat (Triticum aestivum)

AbstractThe percentage of Fusarium‐damaged kernels (FDK) was proposed as a type of Fusarium head blight (FHB) resistance displayed in matured wheat kernels. In this study, Qfdk.nau‐7D, a QTL identified in the Wangshuibai genome for its association with FDK, was introduced into FHB‐susceptible common wheat line PH691 through marker‐assisted selection and backcrossing. Evaluation of two resulted near‐isogenic lines (NILs) showed that the contribution of Qfdk.nau‐7D interval to lower FDK resulted from its effects on resistance to pathogen infection and to disease spread within the spike. Of a few major agronomic traits evaluated, head length was the only one that made difference between PH691 and the NILs. To reduce the QTL interval, a high‐density marker map was constructed using a BC3F2 population of 97 plants. Through resistance evaluation of the homozygous recombinant lines in repeated field trials, Qfdk.nau‐7D, designated as Fhb8, was placed in a 1.0‐cM Xwgrb1500‐Xwgrb1559 interval (from 93.9–96.5 Mb in CS) and showed co‐segregation with Xwgrb1587. Moreover, it was found that the association of Fhb8 with head length was due to close linkage with spike length QTL HL2.

Mapping of qChalk1 controlling grain chalkiness in japonica rice.

Rice grain chalkiness is an undesirable characteristic that affects grain quality. The aim of this study was to map QTLs controlling grain chalkiness in japonica rice. In this study, two japonica rice cultivars with similar grain shapes but different grain chalkiness rates were crossed and the F2 and BC1F2 populations were subjected to QTL-seq analysis to map the QTLs controlling the grain chalkiness rate. QTL-seq analysis revealed SNP index differences on chromosome 1 in both of the segregating populations. Using polymorphic markers between the two parents, QTL mapping was conducted on 213 individual plants in the BC1F2 population. QTL mapping confined a QTL controlling grain chalkiness, qChalk1, to a 1.1Mb genomic region on chromosome 1. qChalk1 explained 19.7% of the phenotypic variation. A QTL controlling grain chalkiness qChalk1 was detected in both F2 and BC1F2 segregating populations by QTL-Seq and QTL mapping methods. This result would be helpful for further cloning of the genes controlling grain chalkiness in japonica rice.

Detection of novel loci involved in non-seed-shattering behaviour of an indica rice cultivar, Oryza sativa IR36

Asian rice (Oryza sativa) was domesticated from O. rufipogon, and reduced seed-shattering behaviour was selected to increase yields. Two seed-shattering loci, qSH3 and sh4, are involved in reducing seed shattering in both japonica and indica rice cultivars, while qSH1 and qCSS3 are likely specific to japonica cultivars. In indica cultivars, qSH3 and sh4 fail to explain the degree of seed shattering, as an introgression line (IL) of O. rufipogon W630 carrying domesticated alleles at qSH3 and sh4 still showed seed shattering. Here we analysed differences in seed-shattering degree between the IL and the indica cultivar IR36. The values for grain detachment in the segregating population between the IL and IR36 were continuous. Based on QTL-seq analysis using the BC1F2 population between the IL and IR36, we detected two novel loci, qCSS2 and qCSS7 (QTLs for the Control of Seed Shattering in rice on chromosomes 2 and 7), which contributed to the reduced seed shattering in IR36. We further investigated the genetic interaction of qCSS2 and qCSS7 under the presence of qSH3 and sh4 mutations in O. rufipogon W630 and found that IL carrying IR36 chromosomal segments covering all four loci are required to explain seed-shattering degree in IR36. Since qCSS2 and qCSS7 were not detected in previous studies on seed shattering in japonica, their control may be specific to indica cultivars. Therefore, they are important to understanding the history of rice domestication as well as to adjusting the seed-shattering degree of indica cultivars to maximise their yield.

Use of exotic Nicotiana tabacum germplasm for confronting an inverse genetic correlation in flue‐cured tobacco

AbstractInverse genetic correlations between cured leaf yields and alkaloid accumulation in flue‐cured tobacco (Nicotiana tabacum L.) complicate the development of higher yielding cultivars while maintaining alkaloids at commercially acceptable levels. Introgression of genomic regions from exotic source material that positively affect alkaloid levels, but with less of a corresponding negative influence on yielding ability, could enhance long‐term efforts to develop improved cultivars. Germplasm accessions “TI 464” and “TI 959” were previously identified as being potentially useful for this purpose. In this study, the relationships between yield and alkaloid accumulation were investigated in BC1F1 populations derived from crosses with these materials and found to be slightly negative or slightly positive. Derived BC1F2 families were used to calculate heritability estimates for alkaloid accumulation on a single plant basis that were low to intermediate in magnitude. The relationships between alkaloid levels of leaves from individual stalk positions and alkaloid levels averaged over all stalk positions were determined. The third stalk position was found to be the most predictive of average alkaloid levels. Selection for alkaloid levels using a single leaf from this stalk position could increase breeding efficiency. BC4F6 lines carrying low genomic contributions from either TI 464 or TI 959 were generated and evaluated as lines per se and in F1 hybrid combinations with a very high‐yielding inbred line with increased leaf number. Performance of these materials indicated that TI 464 and, to a lesser extent TI 959, may be useful for developing higher yielding tobacco cultivars with acceptable alkaloid levels.

Fine mapping and gene silencing pinpoint Capana10g002229 as a strong candidate gene regulating the deciduous character of ripe pepper fruit (Capsicum spp.).

The pepper S locus, which controls the deciduous character of ripe fruit, was first fine mapped into an interval with a physical length of ~ 38.03kb on chromosome P10. Capana10g002229, encoding a polygalacturonase, was proposed as a strong candidate gene based on sequence comparison, expression pattern analysis and virus-induced gene silencing (VIGS). The deciduous character of ripe fruit, which is controlled by the dominant S locus, is a domesticated trait with potential value in the pepper processing industry (Capsicum spp.). However, the gene associated with the S locus has not been identified. Here, one major QTL designated S10.1 was detected by using the F2 population (n = 155) derived from BA3 (Capsicum annuum) × YNXML (Capsicum frutescens) and was further verified in an intraspecific backcross population (n = 254) derived from the cross between BB3 (C. annuum) and its wild relative Chiltepin (C. annuum var. glabriusculum) with BB3 as the recurrent parent. Then, a large BC1F2 population derived from the self-pollination of BB3 × (BB3 × Chiltepin) individuals and comprising 4217 individuals was used to screen the recombinants, and the S locus was ultimately delimited into a 38.03-kb region on chromosome P10 harbouring four annotated genes. Capana10g002229, encoding a polygalacturonase (PG), was proposed as the best candidate gene for S based on sequence comparison and expression pattern analyses. Downregulation of Capana10g002229 in fruits through VIGS significantly delayed fruit softening and abscission from the fruit-receptacle junction. Taken together, the results show that Capana10g002229 could be regarded as a strong candidate gene associated with the S locus in pepper. These findings not only lay a foundation for deciphering the molecular mechanisms underlying pepper domestication but also provide a strategy for genetic improvement of the deciduous character of ripe fruit using a marker-assisted selection approach.

QTL mapping and BSA-seq map a major QTL for the node of the first fruiting branch in cotton.

Understanding the genetic basis of the node of the first fruiting branch (NFFB) improves early-maturity cotton breeding. Here we report QTL mapping on 200 F2 plants and derivative F2:3 and F2:4 populations by genotyping by sequencing (GBS). BC1F2 population was constructed by backcrossing one F2:4 line with the maternal parent JF914 and used for BSA-seq for further QTL mapping. A total of 1,305,642 SNPs were developed between the parents by GBS, and 2,907,790 SNPs were detected by BSA-seq. A high-density genetic map was constructed containing 11,488 SNPs and spanning 4,202.12 cM in length. A total of 13 QTL were mapped in the 3 tested populations. JF914 conferred favorable alleles for 11 QTL, and JF173 conferred favorable alleles for the other 2 QTL. Two stable QTL were repeatedly mapped in F2:3 and F2:4, including qNFFB-D3-1 and qNFFB-D6-1. Only qNFFB-D3-1 contributed more than 10% of the phenotypic variation. This QTL covered about 24.7 Mb (17,130,008-41,839,226 bp) on chromosome D3. Two regions on D3 (41,779,195-41,836,120 bp, 41,836,768-41,872,287 bp) were found by BSA-seq and covered about 92.4 Kb. This 92.4 Kb region overlapped with the stable QTL qNFFB-D3-1 and contained 8 annotated genes. By qRT-PCR, Ghir_D03G012430 showed a lower expression level from the 1- to 2-leaf stage and a higher expression level from the 3- to 6-leaf stage in the buds of JF173 than that of JF914. Ghir_D03G012390 reached the highest level at the 3- and 5-leaf stages in the buds of JF173 and JF914, respectively. As JF173 has lower NFFB and more early maturity than JF914, these two genes might be important in cell division and differentiation during NFFB formation in the seedling stage. The results of this study will facilitate a better understanding of the genetic basis of NFFB and benefit cotton molecular breeding for improving earliness traits.

Genetic analysis and identification of QTLs associated with yield-enhancing traits in Oryza sativa IR64 × Oryza glaberrima interspecific backcross populations

Context Broadening the gene pool of staple food crops by incorporating desirable genes from wild/relative species is way to achieve higher genetic gains. The African rice species Oryza glaberrima Steud. is a source of genes for genetic improvement of Oryza sativa L. to various biotic and abiotic stresses. Aim The study was undertaken to identify genomic regions associated with yield and yield-related traits in interspecific backcross mapping populations derived from variety IR64 (O. sativa indica) × O. glaberrima. Methods The BC1F2 and BC1F2:3 populations were phenotyped for days to 50% flowering, plant height, number of tillers, number of productive tillers, panicle length, spikelet fertility and grain yield under irrigated conditions. The BC1F2 population was genotyped with 99 genome-wide polymorphic SSR markers. Quantitative trait loci (QTLs) associated with yield-enhancing traits were identified through single marker analysis. Key results Significant genetic variability was observed with moderate to high heritability in mapping populations. Genotyping revealed the presence of segregation distortion and skewed genome composition. Single marker analysis identified 20 QTLs linked to the studied traits. A QTL linked to grain yield, qGY-4.1, derived from O. glaberrima was found in both populations with high phenotypic variance. The chromosome region around marker RM510 was identified as a QTL hotspot and putative candidate genes were identified. Conclusions Our study demonstrates that O. glaberrima can serve as a valuable genetic resource for genetic improvement of yield-enhancing traits in O. sativa cultivars. Implications The identified QTLs regions can be employed in molecular breeding. The promising introgression lines identified can be used as pre-breeding lines in future breeding programs.

Genetic variability for plant growth, fruit, seed and biochemical traits in bell pepper breeding populations under North Indian plains

The present research aimed to estimate the plant growth, fruit yield, seed and biochemical traits among the seven pepper parental lines and their six BC2F1 populations in order to generate information regarding the extent of genetic variability, heritability and genetic advance. The study was conducted using a randomized complete block design (RCBD) with three replications at the Vegetable Research Farm of Punjab Agricultural University, Ludhiana, India. The analysis of variance (ANOVA) showed significant mean squares due to parents and BC2F1 populations for almost all the studied traits, it indicating the presence of a sufficient amount of inherent variability among the parental line and developed populations which could be exploited via selection. The plant height, fruit weight, fruit width, number of lobes fruit-1, chlorophyll b, total chlorophyll, chlorophyll a and total fruit yield plant-1 were recorded high GCV and PCV among the parental lines and developed populations BC2F1, indicating higher extent of variability for these traits in the evaluated genotypes. The results revealed that traits with high GCV and PCV offer a better scope for improvement through simple selection. High heritability and high estimates of genetic advance were determined for the traits viz., plant height, fruit weight, ascorbic acid content and total fruit yield plant-1, in both parents and populations. Based on these results, we can conclude that these traits are under the additive gene effects and that above mentioned characters could be considered as a good selection indices in bell pepper.

Genetics of fertility restoration in A2‐based cytoplasmic genetic male sterility system in pigeonpea (Cajanus cajan)

AbstractThe three short duration cytoplasmic genetic male sterility (CGMS) hybrids developed using A2 (Cajanus scarabeoides) cytoplasm‐based male sterile lines (CORG 990047A, CORG 990052A and CORG 7A) and the restorer inbred AK 261322 and their segregating populations (F2 and BC1F1) were subjected to the study of inheritance of fertility restoration in pigeonpea. The fertility restoration was studied based on three different criteria, namely, anther colour, pollen grain fertility and pollen grain morphology and staining. The F2 and BC1F1 populations of the three crosses, namely, CORG 990047A × AK 261322, CORG 990052A × AK 261322 and CORG 7A × AK 261322, segregated in the ratio of 3:1 and 1:1, for anther colour (yellow:pale yellow), pollen grain fertility (fertile:sterile) and for pollen grain morphology and staining. The above study confirmed that the trait fertility restoration was controlled by single dominant gene. This finding can be utilized for the identification of potential restorers, which can be further used in the development of CGMS‐based hybrids in pigeonpea.

Marker-assisted backcross breeding for heat tolerance in bread wheat (Triticum aestivum L.).

Manipulation of flowering time for adaptation through natural or genetic approaches may combat heat-stress damage that occurs at the reproductive stages in production conditions. HD2733, a popular wheat variety of the eastern plains of India, is largely sensitive to heat stress. Therefore, the current study aims to improve heat tolerance of HD2733 by introgression of QTLs associated with early anthesis and high kernel weight linked to markers Xbarc186 and Xgwm190, respectively, through marker-assisted backcross breeding (MABB) from a tolerant donor, WH730. A total of 124 simple sequence repeat (SSR) markers distributed evenly across the genome were used for the background selection. The alleles of Xbarc186 and Xgwm190 were fixed in BC2F1 and BC1F2 generations by selecting individual plants heterozygous for both marker loci and backcrossed with HD2733 and simultaneously selfed to generate BC2F1 and BC1F2 populations, respectively. Furthermore, the selected BC1F2 were selfed to generate the BC1F4 population. By background screening, a total of 39 BC2F3 and 21 BC1F4 families homozygous for the targeted QTLs with 90.9-97.9% and 86.8-88.3% RPG recoveries were selected. The best performing 17 BC2F3 and 10 BC1F4 lines were evaluated for various morpho-physiological traits. Phenotypic evaluation and multi-location trials of the introgressed lines under late sown conditions led to the selection of three promising lines with early anthesis and higher grain yield. The improved lines will serve as an excellent genetic material for functional genomics and expression studies to understand the molecular mechanisms and pathways underlying the stress tolerance.

Assessment of frequency distribution for the morphological and yield related traits in BC1F1, BC2F1 and BC2F2 populations in sweet corn

The nature of gene action and the number of genes controlling the traits are the vital criteria for the selection of traits. The present study is to analyze the range of variations within the population and as well as the skewness and kurtosis in backcross and selfed sweet corn populations USC1-2-3-1× UMI1230β+ and SC1107×UMI1230β+. In the BC2F2 population of SC1107×UMI1230β+, most of the traits showed positive skewness and platykurtic distribution which indicated that complementary gene action  played a role and more number of genes is controlling the traits. In USC1-2-3-1× UMI1230β+, single plant yield recorded positive skewness. In some traits such as, the number of tassel branches, cob girth, and leaf breadth showed negative skewness and platykurtic distribution was also observed in both the cross combination which indicated prevalence of duplicate gene action. In order to fix an individual trait and for rapid genetic gain, duplicate gene action is required.  Keywords: Sweet corn, Skewness, Kurtosis, Gene action.&nbsp

QTL Detection for Rice Grain Length and Fine Mapping of a Novel Locus qGL6.1

BackgroundGrain length (GL) that is directly associated with appearance quality is a key target of selection in rice breeding. Although abundant quantitative trait locus (QTL) associated with GL have been identified, it was still relatively weak to identify QTL for GL from japonica genetic background, as the shortage of japonica germplasms with long grains. We performed QTLs analysis for GL using a recombinant inbred lines (RILs) population derived from the cross between japonica variety GY8 (short grains) and LX1 (long grains) in four environments.ResultsA total of 197 RILs were genotyped with 285 polymorphic SNP markers. Three QTLs qGL5.3, qGL6.1 and qGL11 were detected to control GL by individual environmental analyses and multi-environment joint analysis. Of these, a major-effect and stable QTL qGL6.1 was identified to be a novel QTL, and its LX1 allele had a positive effect on GL. For fine-mapping qGL6.1, a BC1F2 population consisting of 2,487 individuals was developed from a backcross between GY8 and R176, one line with long grain. Eight key informative recombinants were identified by nine kompetitive allele specific PCR (KASP) markers. By analyzing key recombinants, the qGL6.1 locus was narrowed down to a 40.41 kb genomic interval on chromosome 6. One candidate gene LOC_Os06g43304.1 encoding cytochrome P450 (CYP71D55) was finally selected based on the difference in the transcriptional expression and variations in its upstream and downstream region.ConclusionsThree QTLs qGL5.3, qGL6.1 and qGL11 were identified to control grain length in rice. One novel QTL qGL6.1 was fine mapped within 40.41 kb region, and LOC_Os06g43304.1 encoding cytochrome P450 (CYP71D55) may be its candidate gene. We propose that the further cloning of the qGL6.1 will facilitate improving appearance quality in japonica varieties.

Genetic variation of morphological and yield-related traits in backcrossed and selfed population of maize

The number of genes controlling the morphological and yield-related traits and their mode of action plays a vital role in selecting traits and favourable progenies in a segregating population. In this study, we analysed the skewness and kurtosis in the backcrossed and selfed populations of SC11-2×UMI1230β1+. Negative skewness refers to redundant gene activity, positive skewness is connected to complementary gene action. Positive kurtosis suggests the existence of gene activity controlled by a smaller number of genes. Negative kurtosis shows a lack of gene activity and is controlled by a large number of genes. The BC2F2 population of plant height and single plant yield showed positive skewness and platykurtic distribution, suggesting that the genes were governed by complementary gene action and controlled by the large number of genes. This implied need for rigorous selection to achieve a genetic gain in later generations. Cob length and kernel weight showed a duplicate gene action which implied that mild selection can fix these traits and accelerate genetic gain.

Agronomic potential of BC1F2 populations of Santa Cruz dwarf tomato plants

The use of dwarf lines to obtain mini-tomato hybrid plants has led to agronomic and economic advantages. However, the benefits provided by dwarf parents in tomato hybrids of the Santa Cruz type remain unexplored. The aims of this study were to determine the agronomic enhancement in BC1F2 dwarf populations bearing characteristic fruit of the Santa Cruz type after the first backcross and to select populations with high agronomic potential and fruit quality. The experiment was conducted in a greenhouse using a randomized block design with 15 treatments and 4 replicates. Evaluated genetic materials included 11 BC1F2 dwarf tomato populations, both parents (recurrent and donor), and the cultivars (Santa Cruz Kada and Santa Clara). Traits evaluated included: mean weight, soluble solid concentration, number of locules, shape, pulp thickness, fruit longitudinal and transversal diameters, internode length, and plant height. Univariate, multivariate, correlation, and selection index analyses showed that mean fruit weight, transverse diameter, and pulp thickness increased significantly in dwarf populations after a single backcross, most of them exhibiting a fruit shape similar to that of the Santa Cruz type. The dwarf BC1F2 populations UFU-Sci#11 and UFU-Sci#12 showed high potential for obtaining lines and, subsequently, Santa Cruz type hybrids.