scholarly journals The wheat 55K SNP-based exploration of loci for spikelet number per spike from a tetraploid wheat (Triticum turgidum L.) recombinant inbred line population derived from a Chinese landrace ‘Ailanmai’ and a wild emmer accession

2020 ◽  
Author(s):  
Ziqiang Mo ◽  
Jing Zhu ◽  
Jiatai Wei ◽  
Jieguang Zhou ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Genetic Map ◽  
Inbred Line ◽  
Recombinant Inbred ◽  
Snp Array ◽  
Tetraploid Wheat ◽  
Spikelet Number ◽  
Wheat Improvement ◽  
Ril Population ◽  
Spikelet Number Per Spike

AbstractSpikelet number per spike (SNS) is a key factor in determining kernel number per spike which has a great effect on wheat grain yield. Modern wheat breeding narrows genetic diversity among cultivars leading to a detrimental effect on future wheat improvement. It is thus of great significance to explore new genetic resources for SNS to increase wheat yield. Here, a tetraploid landrace ‘Ailanmai’ × wild emmer wheat recombinant inbred line (RIL) population was used to construct a high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. Our results showed that the genetic and physical locations of 94.83% (6204) of the mapped markers were consistent. Subsequently, fourteen quantitative trait loci (QTL) for SNS explaining 4.23-27.26% of the phenotypic variation were identified. QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were considered as major and novel QTL and their combination had the largest effect and increased SNS by 17.47%. In the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, some development-related genes were predicted to participate in the spikelet growth and affect SNS. Additionally, significant correlations between SNS and other agronomic traits like significant and positive correlation between SNS and thousand kernel weight were detected and analyzed. Our findings demonstrated the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat and provided an example of exploring outstanding genetic resources from wheat related species for further utilization in common wheat improvement.Key messageThe wheat 55K SNP array was firstly and successfully applied to construct a genetic map and explore two major and novel QTL for SNS in a tetraploid wheat RIL population.

scholarly journals The Wheat 55K SNP-Based Exploration of Loci for Spikelet Number Per Spike From a Tetraploid Wheat (Triticum Turgidum L.) Recombinant Inbred Line Population Derived From a Chinese Landrace ‘ailanmai’ and a Wild Emmer Accession

2020 ◽  
Author(s):  
Ziqiang Mo ◽  
Jing Zhu ◽  
Jiatai Wei ◽  
Jieguang Zhou ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Genetic Resources ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Wheat Yield ◽  
Snp Array ◽  
Tetraploid Wheat ◽  
Spikelet Number ◽  
Wheat Improvement ◽  
Spikelet Number Per Spike

Abstract Background: Increasing wheat yield is an urgent task to solve the global food shortage. Spikelet number per spike (SNS) is a key factor in determining kernel number per spike which has a great effect on wheat grain yield. However, modern wheat breeding narrows genetic diversity among cultivars leading to a detrimental effect on future wheat improvement. It is thus of great significance to explore new genetic resources for SNS to increase wheat yield.Results: A tetraploid landrace ‘Ailanmai’ × wild emmer wheat recombinant inbred line (RIL) population was used to construct a high-density genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The results showed that 94.83% (6204) of the mapped markers had consistent genetic and physical chromosomal locations. Subsequently, fourteen quantitative trait loci (QTL) for SNS explaining 4.23-27.26% of the phenotypic variation were identified. QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2 were considered as major and novel QTL and their combination had the largest effect and increased SNS by 17.47%. In the physical intervals of QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, some development-related genes were predicted to participate in the spikelet growth and affect SNS. Additionally, significant correlations between SNS and other agronomic traits like significant and positive correlation between SNS and thousand kernel weight were detected and analyzed. Conclusions: Our study demonstrated the feasibility of wheat 55K SNP array in genetic mapping of tetraploid wheat and provided an example of exploring outstanding genetic resources from wheat related species for further utilization in common wheat improvement.

scholarly journals Identification and Validation of a Novel Locus Controlling Spikelet Number in Bread Wheat (Triticum aestivum L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Tao Li ◽  
Guangbing Deng ◽  
Yanyan Tang ◽  
Yan Su ◽  
Jinhui Wang ◽  
...  
Keyword(s):  
Grain Yield ◽  
Genetic Map ◽  
Molecular Mechanisms ◽  
Limit Of Detection ◽  
Expression Patterns ◽  
Snp Array ◽  
Phenotypic Variance ◽  
Spikelet Number ◽  
Grain Number Per Spike ◽  
Spikelet Number Per Spike

Spikelet number is an important target trait for wheat yield improvement. Thus, the identification and verification of novel quantitative trait locus (QTL)/genes controlling spikelet number are essential for dissecting the underlying molecular mechanisms and hence for improving grain yield. In the present study, we constructed a high-density genetic map for the Kechengmai1/Chuanmai42 doubled haploid (DH) population using 13,068 single-nucleotide polymorphism (SNP) markers from the Wheat 55K SNP array. A comparison between the genetic and physical maps indicated high consistence of the marker orders. Based on this genetic map, a total of 27 QTLs associated with total spikelet number per spike (TSN) and fertile spikelet number per spike (FSN) were detected on chromosomes 1B, 1D, 2B, 2D, 3D, 4A, 4D, 5A, 5B, 5D, 6A, 6B, and 7D in five environments. Among them, five QTLs on chromosome 2D, 3D, 5A, and 7D were detected in multiple environments and combined QTL analysis, explaining the phenotypic variance ranging from 3.64% to 23.28%. Particularly, QTsn/Fsn.cib-3D for TSN and FSN [phenotypic variation explained (PVE) = 5.97–23.28%, limit of detection (LOD) = 3.73–18.51] is probably a novel locus and located in a 4.5-cM interval on chromosome arm 3DL flanking by the markers AX-110914105 and AX-109429351. This QTL was further validated in other two populations with different genetic backgrounds using the closely linked Kompetitive Allele-Specific PCR (KASP) marker KASP_AX-110914105. The results indicated that QTsn/Fsn.cib-3D significantly increased the TSN (5.56–7.96%) and FSN (5.13–9.35%), which were significantly correlated with grain number per spike (GNS). We also preliminary analyzed the candidate genes within this locus by sequence similarity, spatial expression patterns, and collinearity analysis. These results provide solid foundation for future fine mapping and cloning of QTsn/Fsn.cib-3D. The developed and validated KASP markers could be utilized in molecular breeding aiming to increase the grain yield in wheat.

scholarly journals The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace “Ailanmai” × Wild Emmer

2021 ◽  
Vol 12 ◽  
Author(s):  
Ziqiang Mo ◽  
Jing Zhu ◽  
Jiatai Wei ◽  
Jieguang Zhou ◽  
Qiang Xu ◽  
...  
Keyword(s):  
Common Wheat ◽  
Agronomic Traits ◽  
Wheat Yield ◽  
Snp Array ◽  
Tetraploid Wheat ◽  
Wild Emmer ◽  
Potential Candidate ◽  
Spikelet Number ◽  
Improvement Programs ◽  
Spikelet Number Per Spike

Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace “Ailanmai” × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71–29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.

scholarly journals Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1690
Author(s):  
Yheni Dwiningsih ◽  
Anuj Kumar ◽  
Julie Thomas ◽  
Charles Ruiz ◽  
Jawaher Alkahtani ◽  
...  
Keyword(s):  
Candidate Genes ◽  
High Throughput ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Genetic Information ◽  
Snp Markers ◽  
Rice Grain ◽  
Grain Length ◽  
Ril Population

Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of “Kaybonnet (KBNT lpa)” and “ZHE733” named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.

scholarly journals Genetic loci mapping for ear axis weight using recombinant inbred line (RIL) population under different nitrogen regimes in maize

2011 ◽  
Vol 10 (42) ◽  
pp. 8255-8259 ◽  
Author(s):  
Zheng Zu Ping ◽  
Liu Xiao Hong ◽  
Wu Xun ◽  
Zhang Yong Si ◽  
He Chuan
Keyword(s):  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Recombinant Inbred ◽  
Genetic Loci ◽  
Ril Population

scholarly journals Mapping of QTL for total spikelet number per spike on chromosome 2D in wheat using a high-density genetic map

2019 ◽  
Vol 42 (3) ◽  
pp. 603-610 ◽  
Author(s):  
Mei Deng ◽  
Fangkun Wu ◽  
Wanlin Zhou ◽  
Jing Li ◽  
Haoran Shi ◽  
...  
Keyword(s):  
Genetic Map ◽  
High Density ◽  
Spikelet Number ◽  
Spikelet Number Per Spike

Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.)

2015 ◽  
Vol 95 (6) ◽  
pp. 1133-1144
Author(s):  
R. Khanal ◽  
A. Navabi ◽  
L. Lukens
Keyword(s):  
Quantitative Trait Loci ◽  
Qtl Mapping ◽  
Linkage Map ◽  
Inbred Line ◽  
Recombinant Inbred Line ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Map Construction ◽  
Ril Population ◽  
Trait Loci

Khanal, R., Navabi, A. and Lukens, L. 2015. Linkage map construction and quantitative trait loci (QTL) mapping using intermated vs. selfed recombinant inbred maize line (Zea mays L.). Can. J. Plant Sci. 95: 1133–1144. Intermating of individuals in an F2 population increases genetic recombination between markers, which is useful for linkage map construction and quantitative trait loci (QTL) mapping. The objectives of this study were to compare the linkage maps and precision of QTL detection in an intermated recombinant inbred line (IRIL) population and a selfed recombinant inbred line (RIL) population. Both, IRIL and RIL, populations were developed from Zea mays inbred lines CG60 and CG102. The populations were grown in two environments to evaluate traits, and inbred lines from each population were genotyped with SSR and SNP markers for linkage map construction and QTL identification. In addition, we simulated RIL and IRIL populations from two inbred parents to compare the precision of QTL detection between simulated RIL and IRIL populations. In the empirical study, the linkage map was longer in RIL as compared with IRIL, and the average QTL support interval was reduced by 1.37-fold in the IRIL population compared with the RIL population. We detected 16 QTL for flowering time, plant height, leaf number, and stay green in at least one recombinant inbred line population. Two out of 16 QTL were shared between two recombinant inbred line populations. In the simulation study, the QTL support interval was reduced by 1.66-fold in the IRIL population as compared with the RIL population and linked QTL were identified more frequently in IRIL population as compared with RIL population. This study supports the utility of intermated RIL populations for precise QTL mapping.

scholarly journals Genetic Analysis of Recombinant Inbred Lines for Sorghum bicolor × Sorghum propinquum

2013 ◽  
Vol 3 (1) ◽  
pp. 101-108 ◽  
Author(s):  
Wenqian Kong ◽  
Huizhe Jin ◽  
Cleve D Franks ◽  
Changsoo Kim ◽  
Rajib Bandopadhyay ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Sorghum Bicolor ◽  
Genetic Map ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Growth And Development ◽  
Recombinant Inbred Lines ◽  
Sorghum Propinquum ◽  
Ril Population ◽  
Trait Loci

Abstract We describe a recombinant inbred line (RIL) population of 161 F5 genotypes for the widest euploid cross that can be made to cultivated sorghum (Sorghum bicolor) using conventional techniques, S. bicolor × Sorghum propinquum, that segregates for many traits related to plant architecture, growth and development, reproduction, and life history. The genetic map of the S. bicolor × S. propinquum RILs contains 141 loci on 10 linkage groups collectively spanning 773.1 cM. Although the genetic map has DNA marker density well-suited to quantitative trait loci mapping and samples most of the genome, our previous observations that sorghum pericentromeric heterochromatin is recalcitrant to recombination is highlighted by the finding that the vast majority of recombination in sorghum is concentrated in small regions of euchromatin that are distal to most chromosomes. The advancement of the RIL population in an environment to which the S. bicolor parent was well adapted (indeed bred for) but the S. propinquum parent was not largely eliminated an allele for short-day flowering that confounded many other traits, for example, permitting us to map new quantitative trait loci for flowering that previously eluded detection. Additional recombination that has accrued in the development of this RIL population also may have improved resolution of apices of heterozygote excess, accounting for their greater abundance in the F5 than the F2 generation. The S. bicolor × S. propinquum RIL population offers advantages over early-generation populations that will shed new light on genetic, environmental, and physiological/biochemical factors that regulate plant growth and development.

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