Quantitative traits loci mapping and molecular marker development for total glutenin and glutenin fraction contents in wheat

Abstract Background Glutenin contents and compositions are crucial factors influencing the end-use quality of wheat. Although the composition of glutenin fractions is well known, there has been relatively little research on the genetic basis of glutenin fractions in wheat. Results To elucidate the genetic basis for the contents of glutenin and its fractions, a population comprising 196 recombinant inbred lines (RILs) was constructed from two parents, Luozhen No.1 and Zhengyumai 9987, which differ regarding their total glutenin and its fraction contents (except for the By fraction). Forty-one additive Quantitative Trait Loci (QTL) were detected in four environments over two years. These QTL explained 1.3% - 53.4% of the phenotypic variation in the examined traits. Forty-three pairs of epistatic QTL (E-QTL) were detected in the RIL population across four environments. The QTL controlling the content of total glutenin and its seven fractions were detected in clusters. Seven clusters enriched with QTL for more than three traits were identified, including a QTL cluster 6AS-3, which was revealed as a novel genetic locus for glutenin and related traits. Kompetitive Allele-Specific PCR (KASP) markers developed from the main QTL cluster 1DL-2 and the previously developed KASP marker for the QTL cluster 6AS-3 were validated as significantly associated with the target traits in the RIL population and in natural varieties. Conclusions This study identified novel genetic loci related to glutenin and its seven fractions. Additionally, the developed KASP markers may be useful for the marker-assisted selection of varieties with high glutenin fraction content and for identifying individuals in the early developmental stages without the need for phenotyping mature plants. On the basis of the results of this study and the KASP markers described herein, breeders will be able to efficiently select wheat lines with favorable glutenin properties and develop elite lines with high glutenin subunit contents.

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QTL Mapping and Validation for Kernel Area and Circumference in Common Wheat via High-Density SNP-Based Genotyping

Frontiers in Plant Science ◽

10.3389/fpls.2021.713890 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tianheng Ren ◽

Tao Fan ◽

Shulin Chen ◽

Xia Ou ◽

Yongyan Chen ◽

...

Keyword(s):

Recombinant Inbred Lines ◽

Snp Array ◽

Interval Mapping ◽

Mapping Method ◽

Kernel Weight ◽

Kernel Size ◽

Specific Pcr ◽

Wheat Kernel ◽

Ril Population ◽

Stable Qtls

As an important component, 1,000 kernel weight (TKW) plays a significant role in the formation of yield traits of wheat. Kernel size is significantly positively correlated to TKW. Although numerous loci for kernel size in wheat have been reported, our knowledge on loci for kernel area (KA) and kernel circumference (KC) remains limited. In the present study, a recombinant inbred lines (RIL) population containing 371 lines genotyped using the Wheat55K SNP array was used to map quantitative trait loci (QTLs) controlling the KA and KC in multiple environments. A total of 54 and 44 QTLs were mapped by using the biparental population or multienvironment trial module of the inclusive composite interval mapping method, respectively. Twenty-two QTLs were considered major QTLs. BLAST analysis showed that major and stable QTLs QKc.sau-6A.1 (23.12–31.64 cM on 6A) for KC and QKa.sau-6A.2 (66.00–66.57 cM on 6A) for KA were likely novel QTLs, which explained 22.25 and 20.34% of the phenotypic variation on average in the 3 year experiments, respectively. Two Kompetitive allele-specific PCR (KASP) markers, KASP-AX-109894590 and KASP-AX-109380327, were developed and tightly linked to QKc.sau-6A.1 and QKa.sau-6A.2, respectively, and the genetic effects of the different genotypes in the RIL population were successfully confirmed. Furthermore, in the interval where QKa.sau-6A.2 was located on Chinese Spring and T. Turgidum ssp. dicoccoides reference genomes, only 11 genes were found. In addition, digenic epistatic QTLs also showed a significant influence on KC and KA. Altogether, the results revealed the genetic basis of KA and KC and will be useful for the marker-assisted selection of lines with different kernel sizes, laying the foundation for the fine mapping and cloning of the gene(s) underlying the stable QTLs detected in this study.

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Analysis of genetic control and QTL mapping of essential wheat grain quality traits in a recombinant inbred population

10.1101/361329 ◽

2018 ◽

Author(s):

Sonia Goel ◽

Kalpana Singh ◽

Balwant Singh ◽

Sapna Grewal ◽

Neeta Dwivedi ◽

...

Keyword(s):

Recombinant Inbred ◽

Recombinant Inbred Lines ◽

Transgressive Segregation ◽

Quality Traits ◽

Bread Making ◽

Recombinant Inbred Population ◽

Ril Population ◽

End Use ◽

Baking Industry ◽

New Alleles

AbstractWheat cultivars are genetically crossed for improving end use quality for apt traits as per need of baking industry and broad consumer’s preferences. The processing and baking qualities of bread wheat underlie into genetic make-up of a variety and influence by environmental factors and their interactions. WL711 and C306 derived recombinant inbred lines (RILs) population of 206 was used for phenotyping of quality related traits in three different environmental conditions. The genetic analysis of quality traits showed considerable variation for measurable quality traits with normal distribution and transgressive segregation across the years. From the 206 RIL, few RILs found to be superior to those of the parental cultivars for key quality traitsindicating their potential usefor improvement of end use quality and also suggestingprobability of finding new alleles and allelic combinations from the RIL population. A genetic linkage map including 346 markers was constructed withtotal map distance of 4526.8cM andinterval distance between adjacent markersof 12.9cM. Mapping analysis identified 38 putative QTLs for 13 quality related traits with QTLs explaining 7.9% - 16.8% phenotypic variation spanning over 14 chromosomes i.e. 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. Major novel QTLs regions for quality traits have been identified on several chromosome in studied RIL population posing their potential role in marker assisted selection for better bread making quality after validation.

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Recombinant inbred lines derived from cultivars of pea for understanding the genetic basis of variation in breeders' traits

Plant Genetic Resources ◽

10.1017/s1479262118000345 ◽

2018 ◽

Vol 16 (5) ◽

pp. 424-436 ◽

Cited By ~ 3

Author(s):

Carol Moreau ◽

Maggie Knox ◽

Lynda Turner ◽

Tracey Rayner ◽

Jane Thomas ◽

...

Keyword(s):

Recombinant Inbred ◽

Seed Weight ◽

Genetic Basis ◽

Recombinant Inbred Lines ◽

Field Trials ◽

Genetic Maps ◽

Genotypic Differences ◽

Phenotypic Data ◽

Growing Seasons ◽

Randomized Field Trials

AbstractIn order to gain an understanding of the genetic basis of traits of interest to breeders, the pea varieties Brutus, Enigma and Kahuna were selected, based on measures of their phenotypic and genotypic differences, for the construction of recombinant inbred populations. Reciprocal crosses were carried out for each of the three pairs, and over 200 F2 seeds from each cross advanced to F13. Bulked F7 seeds were used to generate F8–F11 bulks, which were grown in triplicated plots within randomized field trials and used to collect phenotypic data, including seed weight and yield traits, over a number of growing seasons. Genetic maps were constructed from the F6 generation to support the analysis of qualitative and quantitative traits and have led to the identification of four major genetic loci involved in seed weight determination and at least one major locus responsible for variation in yield. Three of the seed weight loci, at least one of which has not been described previously, were associated with the marrowfat seed phenotype. For some of the loci identified, candidate genes have been identified. The F13 single seed descent lines are available as a germplasm resource for the legume and pulse crop communities.

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Fine Mapping of qd1, a Dominant Gene that Regulates Stem Elongation in Bread Wheat

Frontiers in Genetics ◽

10.3389/fgene.2021.793572 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yongdun Xie ◽

Weiwei Zeng ◽

Chaojie Wang ◽

Daxing Xu ◽

Huijun Guo ◽

...

Keyword(s):

Bread Wheat ◽

Stem Elongation ◽

Dominant Gene ◽

Nucleotide Polymorphisms ◽

Sequencing Data ◽

Specific Pcr ◽

Yield Determination ◽

Allele Specific ◽

Stem Development ◽

Kasp Markers

Stem elongation is a critical phase for yield determination and, as a major trait, is targeted for manipulation for improvement in bread wheat (Triticum aestivum L.). In a previous study, we characterized a mutant showing rapid stem elongation but with no effect on plant height at maturity. The present study aimed to finely map the underlying mutated gene, qd1, in this mutant. By analyzing an F2 segregating population consisting of 606 individuals, we found that the qd1 gene behaved in a dominant manner. Moreover, by using the bulked segregant RNA sequencing (BSR-seq)-based linkage analysis method, we initially mapped the qd1 gene to a 13.55 Mb region on chromosome 4B (from 15.41 to 28.96 Mb). This result was further confirmed in F2 and BC3F2 segregating populations. Furthermore, by using transcriptome sequencing data, we developed 14 Kompetitive Allele-Specific PCR (KASP) markers and then mapped the qd1 gene to a smaller and more precise 5.08 Mb interval from 26.80 to 31.88 Mb. To develop additional markers to finely map the qd1 gene, a total of 4,481 single-nucleotide polymorphisms (SNPs) within the 5.08 Mb interval were screened, and 25 KASP markers were developed based on 10x-depth genome resequencing data from both wild-type (WT) and mutant plants. The qd1 gene was finally mapped to a 1.33 Mb interval from 28.86 to 30.19 Mb on chromosome 4B. Four candidate genes were identified in this region. Among them, the expression pattern of only TraesCS4B02G042300 in the stems was concurrent with the stem development of the mutant and WT. The qd1 gene could be used in conjunction with molecular markers to manipulate stem development in the future.

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Impact of epistasis and QTL×environment interaction on the accumulation of seed mass of soybean (Glycine max L. Merr.)

Genetics Research ◽

10.1017/s0016672308009865 ◽

2008 ◽

Vol 90 (6) ◽

pp. 481-491 ◽

Cited By ~ 20

Author(s):

YINGPENG HAN ◽

WEILI TENG ◽

DESHENG SUN ◽

YUPING DU ◽

LIJUAN QIU ◽

...

Keyword(s):

Seed Development ◽

Seed Weight ◽

Developmental Stages ◽

Environmental Control ◽

Recombinant Inbred Lines ◽

Seed Mass ◽

Environment Interaction ◽

Glycine Max L ◽

Trait Locus ◽

100 Seed Weight

SummaryThe accumulation of seed mass in soybean is affected by both genotype and environment. The aim of the present study was to measure additive, epistatic and quantitative trait locus (QTL)×environment (QE) interaction effects of QTLs on the development of 100-seed weight in a population of 143 F5 derived recombinant inbred lines (RILs) developed from the cross between the soybean cultivars ‘Charleston’ and ‘Dong Nong 594’. Broad-sense heritability of 100-seed weight from 30 days (30D) to 80D stages was 0·58, 0·52, 0·62, 0·60, 0·66 and 0·57, respectively. A total of 17 QTLs with conditional additive (a) effect and/or conditional additive×environment interaction (ae) effect at specific stages were identified in ten linkage groups by conditional mapping. Of them, only 4 QTLs had significant a effect or ae effect at different stages of seed development. Among QTLs with significant a effect, five acted positively and six acted negatively on seed development. A total of 35 epistatic pairwise QTLs of 100-seed weight were identified by conditional mapping at different developmental stages. Five pairs of QTL showed the additive×additive epistatic (aa) effect and 16 QTLs showed the aa×environment interaction (aae) effect at the different developmental stages. QTLs with aa effect as well with their environmental interaction effect appeared to vary at different developmental stages. Overall, the results indicated that 100-seed weight in soybean is under developmental, genetic and environmental control.

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Genetic dissection of yield-related traits and mid-parent heterosis for those traits in maize (Zea mays L.)

BMC Plant Biology ◽

10.1186/s12870-019-2009-2 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 4

Author(s):

Qiang Yi ◽

Yinghong Liu ◽

Xianbin Hou ◽

Xiangge Zhang ◽

Hui Li ◽

...

Keyword(s):

Genetic Basis ◽

Recombinant Inbred Lines ◽

Kernel Weight ◽

Genetic Dissection ◽

Hybrid Mapping ◽

Maize Breeding ◽

Phenotypic Variations ◽

Selection For ◽

Genomic Regions ◽

Mapping Populations

Abstract Background Utilization of heterosis in maize could be critical in maize breeding for boosting grain yield. However, the genetic architecture of heterosis is not fully understood. To dissect the genetic basis of yield-related traits and heterosis in maize, 301 recombinant inbred lines derived from 08 to 641 × YE478 and 298 hybrids from the immortalized F2 (IF2) population were used to map quantitative trait loci (QTLs) for nine yield-related traits and mid-parent heterosis. Results We observed 156 QTLs, 28 pairs of loci with epistatic interaction, and 10 significant QTL × environment interactions in the inbred and hybrid mapping populations. The high heterosis in F1 and IF2 populations for kernel weight per ear (KWPE), ear weight per ear (EWPE), and kernel number per row (KNPR) matched the high percentages of QTLs (over 50%) for those traits exhibiting overdominance, whereas a notable predominance of loci with dominance effects (more than 70%) was observed for traits that show low heterosis such as cob weight per ear (CWPE), rate of kernel production (RKP), ear length (EL), ear diameter (ED), cob diameter, and row number (RN). The environmentally stable QTL qRKP3–2 was identified across two mapping populations, while qKWPE9, affecting the trait mean and the mid-parent heterosis (MPH) level, explained over 18% of phenotypic variations. Nine QTLs, qEWPE9–1, qEWPE10–1, qCWPE6, qEL8, qED2–2, qRN10–1, qKWPE9, qKWPE10–1, and qRKP4–3, accounted for over 10% of phenotypic variation. In addition, QTL mapping identified 95 QTLs that were gathered together and integrated into 33 QTL clusters on 10 chromosomes. Conclusions The results revealed that (1) the inheritance of yield-related traits and MPH in the heterotic pattern improved Reid (PA) × Tem-tropic I (PB) is trait-dependent; (2) a large proportion of loci showed dominance effects, whereas overdominance also contributed to MPH for KNPR, EWPE, and KWPE; (3) marker-assisted selection for markers at genomic regions 1.09–1.11, 2.04, 3.08–3.09, and 10.04–10.05 contributed to hybrid performance per se and heterosis and were repeatedly reported in previous studies using different heterotic patterns is recommended.

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Impact of epistasis and QTL×environmental interaction on the mass filling rate during seed development of soybean

Genetics Research ◽

10.1017/s0016672312000286 ◽

2012 ◽

Vol 94 (2) ◽

pp. 63-71 ◽

Cited By ~ 4

Author(s):

ZHENFENG JIANG ◽

YINGPENG HAN ◽

WEILI TENG ◽

YONGGUANG LI ◽

XUE ZHAO ◽

...

Keyword(s):

Seed Development ◽

Developmental Stages ◽

Environmental Control ◽

Recombinant Inbred Lines ◽

Soybean Seed ◽

Environment Interaction ◽

Filling Rate ◽

Seed Filling ◽

Environment Effects ◽

Initial Stage

SummarySeed filling rate of soybean has been shown to be a dynamic process in different developmental stages affected by both genotype and environment. The objective of the present study was to determine additive, epistatic and quantitative trait loci (QTLs)×environment interaction (QE) effects of the QTL underlying a seed filling rate of soybean. One hundred and forty-three recombinant inbred lines (RILs) derived from the cross of Charleston and Dongnong 594 were used with 2 years of field data (2004 and 2005). Eleven QTLs with significantly unconditional and conditional additive (a) effect and/or additive×environment interaction (ae) effect at different filling stages were identified. Of them six QTLs showed positive a effects and four QTLs had negative a effects on the seed filling rate during seed development. aa and aae effects of 12 pairs of QTLs were identified by unconditional mapping from the initial stage to the final stage. Thirteen pairs of QTLs underlying the seed filling rate with aa and aae effects were identified by conditional mapping. QTLs with aa and aae (additive×additive×environment) effects appeared to vary at different filling stages. Our results demonstrated that the mass filling rate in soybean seed were under genetic and environmental control.

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Genetic basis of body color and spotting pattern in redheaded pine sawfly larvae (Neodiprion lecontei)

10.1101/183996 ◽

2017 ◽

Author(s):

Catherine R. Linnen ◽

Claire T. O’Quin ◽

Taylor Shackleford ◽

Connor R. Sears ◽

Carita Lindstedt

Keyword(s):

Genetic Basis ◽

Developmental Stages ◽

Color Variation ◽

Body Color ◽

Sawfly Larvae ◽

Pine Sawfly ◽

Neodiprion Lecontei ◽

Yellow Body ◽

In The Wild ◽

Trait Locus

ABSTRACTPigmentation has emerged as a premier model for understanding the genetic basis of phenotypic evolution, and a growing catalog of color loci is starting to reveal biases in the mutations, genes, and genetic architectures underlying color variation in the wild. However, existing studies have sampled a limited subset of taxa, color traits, and developmental stages. To expand our sample of color loci, we performed quantitative trait locus (QTL) mapping analyses on two types of larval pigmentation traits that vary among populations of the redheaded pine sawfly (Neodiprion lecontei): carotenoid-based yellow body color and melanin-based spotting pattern. For both traits, our QTL models explained a substantial proportion of phenotypic variation and suggested a genetic architecture that is neither monogenic nor highly polygenic. Additionally, we used our linkage map to anchor the current N. lecontei genome assembly. With these data, we identified promising candidate genes underlying: (1) a loss of yellow pigmentation in Mid-Atlantic/northeastern populations (Cameo2 and apoLTP-II/I), and (2) a pronounced reduction in black spotting in Great-Lakes populations (yellow, TH, Dat). Several of these genes also contribute to color variation in other wild and domesticated taxa. Overall, our findings are consistent with the hypothesis that predictable genes of large-effect contribute to color evolution in nature.

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Genetic Basis for Lipopolysaccharide O-Antigen Biosynthesis in Bordetellae

Infection and Immunity ◽

10.1128/iai.67.8.3763-3767.1999 ◽

1999 ◽

Vol 67 (8) ◽

pp. 3763-3767 ◽

Cited By ~ 64

Author(s):

Andrew Preston ◽

Andrew G. Allen ◽

Joanna Cadisch ◽

Richard Thomas ◽

Kim Stevens ◽

...

Keyword(s):

Insertion Sequence ◽

Genetic Basis ◽

Genetic Locus ◽

Bordetella Bronchiseptica ◽

Open Reading Frames ◽

Bordetella Parapertussis ◽

O Antigen ◽

Surface Polysaccharide ◽

Reading Frames

ABSTRACT Bordetella bronchiseptica and Bordetella parapertussis express a surface polysaccharide, attached to a lipopolysaccharide, which has been called O antigen. This structure is absent from Bordetella pertussis. We report the identification of a large genetic locus in B. bronchiseptica and B. parapertussis that is required for O-antigen biosynthesis. The locus is replaced by an insertion sequence in B. pertussis, explaining the lack of O-antigen biosynthesis in this species. The DNA sequence of the B. bronchiseptica locus has been determined and the presence of 21 open reading frames has been revealed. We have ascribed putative functions to many of these open reading frames based on database searches. Mutations in the locus in B. bronchiseptica andB. parapertussis prevent O-antigen biosynthesis and provide tools for the study of the role of O antigen in infections caused by these bacteria.

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Genotyping by sequencing of 393 Sorghum bicolor BTx623 × IS3620C recombinant inbred lines improves sensitivity and resolution of QTL detection

10.1101/308478 ◽

2018 ◽

Author(s):

WenQian Kong ◽

Changsoo Kim ◽

Dong Zhang ◽

Hui Guo ◽

Xu Tan ◽

...

Keyword(s):

Flowering Time ◽

Plant Height ◽

Recombinant Inbred ◽

Recombinant Inbred Lines ◽

Genotyping By Sequencing ◽

Snp Markers ◽

Ril Population ◽

Trait Locus ◽

Number Of Individuals ◽

Syntenic Regions

AbstractWe describe a genetic map with a total of 381 bins of 616 genotyping by sequencing (GBS)-based SNP markers in a F6-F8 recombinant inbred line (RIL) population of 393 individuals derived from crossing S. bicolor BTx623 to S. bicolor IS3620C, a guinea line substantially diverged from BTx623. Five segregation distorted regions were found with four showing enrichment for S. bicolor alleles, suggesting possible selection during formation of this RIL population. A quantitative trait locus (QTL) study with this number of individuals, tripled relative to prior studies of this cross, provided resources, validated previous findings, and demonstrated improved power to detect plant height and flowering time related QTLs relative to other published studies. An unexpected low correlation between flowering time and plant height permitted us to separate QTLs for each trait and provide evidence against pleiotropy. Ten non-random syntenic regions conferring QTLs for the same trait suggest that those QTLs may represent alleles at genes functioning in the same manner since the 96 million year ago genome duplication that created these syntenic relationships, while syntenic regions conferring QTLs for different trait may suggest sub-functionalization after duplication. Collectively, this study provides resources for marker-assisted breeding, as well as a framework for fine mapping and subsequent cloning of major genes for important traits such as plant height and flowering time in sorghum.

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