scholarly journals QTL Analysis of Domestication Syndrome in Zombi Pea (Vigna vexillata), an Underutilized Legume Crop

2018 ◽  
Author(s):  
Sujinna Dachapak ◽  
Norihiko Tomooka ◽  
Prakit Somta ◽  
Ken Naito ◽  
Akito Kaga ◽  
...  
Keyword(s):  
Linkage Map ◽  
Seed Size ◽  
Qtl Analysis ◽  
Leaf Size ◽  
Interval Mapping ◽  
Linkage Groups ◽  
Legume Crop ◽  
Vigna Vexillata ◽  
Length Width ◽  
Trait Locus

AbstractZombi pea (Vigna vexillata (L.) A. Rich) is an underutilized crop belonging to the genus Vigna. Two domesticated forms of zombi pea are cultivated as crop plants; seed and tuber forms. The cultivated seed form is present in Africa, while the cultivated tuber form is present in a very limited part of Asia. Genetics of domestication have been investigated in most of cultivated Vigna crops by means of quantitative trait locus (QTL) mapping. In this study, we investigated genetics of domestication in zombi pea by QTL analysis using an F2 population of 139 plants derived from a cross between cultivated tuber form of V. vexillata (JP235863) and wild V. vexillata (AusTRCF66514). A linkage map with 11 linkage groups was constructed from this F2 population using 145 SSR, 117 RAD-seq and 2 morphological markers. Many highly segregation distorted markers were found on LGs 5, 6, 7, 8, 10 and 11. Most of the distorted markers were clustered together and all the markers on LG8 were highly distorted markers. Comparing this V. vexillata linkage map with a previous linkage map of V. vexillata and linkage maps of other four Vigna species demonstrated several macro translocations in V. vexillata. QTL analysis for 22 domestication-related traits was investigated by inclusive composite interval mapping in which 37 QTLs were identified for 18 traits; no QTL was detected for 4 traits. Number of QTLs detected in each trait ranged from 1 to 5 with an average of only 2.3. Tuber traits were controlled by five QTLs with similar effect locating on different linkage groups. Large-effect QTLs (PVE > 20%) were on LG4 (pod length), LG5 (leaf size and seed thickness), and LG7 (for seed-related traits). Comparison of domestication-related QTLs of the zombi pea with those of cowpea (Vigna unguiculata), azuki bean (Vigna angularis), mungbean (Vigna radiata) and rice bean (Vigna umbellata) revealed that there was conservation of some QTLs for seed size, pod size and leaf size between zombi pea and cowpea and that QTLs associated with seed size (weight, length, width and thickness) in each species were clustered on same linkage.

scholarly journals A new intervarietal linkage map and its application for quantitative trait locus analysis of "gigas" features in bread wheat

Genome ◽  
2005 ◽  
Vol 48 (1) ◽  
pp. 65-75 ◽  
Author(s):  
Kazuhiro Suenaga ◽  
Mireille Khairallah ◽  
H M William ◽  
David A Hoisington
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Map ◽  
Qtl Analysis ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Spike Number ◽  
Trait Locus ◽  
Dh Lines ◽  
Simple Sequence

A doubled-haploid (DH) population from an intervarietal cross between the Japanese cultivar 'Fukuho-komugi' and the Israeli wheat line 'Oligoculm' was produced by means of wheat × maize crosses. One hundred seven DH lines were genotyped to construct a simple sequence repeat (SSR) based linkage map with RFLP, RAPD, and inter-simple sequence repeat markers. Out of 570 loci genotyped, 330 were chosen based on their positions on the linkage map to create a "framework" map for quantitative trait locus (QTL) analysis. Among the 28 linkage groups identified, 25 were assigned to the 21 chromosomes of wheat. The total map length was 3948 cM, including the three unassigned linkage groups (88 cM), and the mean interval between loci was 12.0 cM. Loci with segregation distortion were clustered on chromosomes 1A, 4B, 4D, 5A, 6A, 6B, and 6D. After vernalization, the DH lines were evaluated for spike number per plant (SN) and spike length (SL) in a greenhouse under 24-h daylength to assess the "gigas" features (extremely large spikes and leaves) of 'Oligoculm'. The DH lines were also autumn-sown in the field in two seasons (1990–1991 and 1997–1998) for SN and SL evaluation. QTL analysis was performed by composite interval mapping (CIM) with the framework map to detect QTLs for SN and SL. A major QTL on 1AS, which was stable in both greenhouse and field conditions, was found to control SN. This QTL was close to the glume pubescence locus (Hg) and explained up to 62.9% of the total phenotypic variation. The 'Oligoculm' allele restricted spike number. The SSR locus Xpsp2999 was the closest locus to this QTL and is considered to be a possible marker for restricted tillering derived from 'Oligoculm'. Eight QTLs were detected for SL. The largest QTL detected on 2DS was common to the greenhouse and field environments. It explained up to 33.3% of the total phenotypic variation. The second largest QTL on 1AS was common to the greenhouse and the 1997–1998 season. The position of this QTL was close to that for the SN detected on 1AS. The association between SN and SL is discussed.Key words: linkage map, microsatellite, QTL, spike length, spike number.

scholarly journals Quantitative Trait Locus Analysis in Avocado: The Challenge of a Slow-maturing Horticultural Tree Crop

2019 ◽  
Vol 144 (5) ◽  
pp. 352-362
Author(s):  
Vanessa E.T.M. Ashworth ◽  
Haofeng Chen ◽  
Carlos L. Calderón-Vázquez ◽  
Mary Lu Arpaia ◽  
David N. Kuhn ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Linkage Group ◽  
Linkage Map ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
Persea Americana ◽  
Phenotypic Traits ◽  
Experimental Population ◽  
Tree Crop ◽  
Trait Locus

The glossy, green-fleshed fruit of the avocado (Persea americana) has been the object of human selection for thousands of years. Recent interest in healthy nutrition has singled out the avocado as an excellent source of several phytonutrients. Yet as a sizeable, slow-maturing tree crop, it has been largely neglected by genetic studies, owing to a long breeding cycle and costly field trials. We use a small, replicated experimental population of 50 progeny, grown at two locations in two successive years, to explore the feasibility of developing a dense genetic linkage map and to implement quantitative trait locus (QTL) analysis for seven phenotypic traits. Additionally, we test the utility of candidate-gene single-nucleotide polymorphisms developed to genes from biosynthetic pathways of phytonutrients beneficial to human health. The resulting linkage map consisted of 1346 markers (1044.7 cM) distributed across 12 linkage groups. Numerous markers on Linkage Group 10 were associated with a QTL for flowering type. One marker on Linkage Group 1 tracked a QTL for β-sitosterol content of the fruit. A region on Linkage Group 3 tracked vitamin E (α-tocopherol) content of the fruit, and several markers were stable across both locations and study years. We argue that the pursuit of linkage mapping and QTL analysis is worthwhile, even when population size is small.

Regression based fast multi-trait genome-wide QTL analysis

2021 ◽  
pp. 2050044
Author(s):  
Md. Jahangir Alam ◽  
Md. Ripter Hossain ◽  
S. M. Shahinul Islam ◽  
Md. Nurul Haque Mollah
Keyword(s):  
Qtl Analysis ◽  
Expectation Maximization ◽  
Computation Time ◽  
Interval Mapping ◽  
Multivariate Normal ◽  
New Approach ◽  
Multiple Quantitative Trait Locus ◽  
Genome Wide ◽  
Complex Process ◽  
Trait Locus

Multivariate simple interval mapping (SIM) is one of the most popular approaches for multiple quantitative trait locus (QTL) analysis. Both maximum likelihood (ML) and least squares (LS) multivariate regression (MVR) are widely used methods for multi-trait SIM. ML-based MVR (MVR-ML) is an expectation maximization (EM) algorithm based iterative and complex time-consuming approach. Although the LS-based MVR (MVR-LS) approach is not an iterative process, the calculation of likelihood ratio (LR) statistic in MVR-LS is also a time-consuming complex process. We have introduced a new approach (called FastMtQTL) for multi-trait QTL analysis based on the assumption of multivariate normal distribution of phenotypic observations. Our proposed method can identify almost the same QTL positions as those identified by the existing methods. Moreover, the proposed method takes comparatively less computation time because of the simplicity in the calculation of LR statistic by this method. In the proposed method, LR statistic is calculated only using the sample variance–covariance matrix of phenotypes and the conditional probability of QTL genotype given the marker genotypes. This improvement in computation time is advantageous when the numbers of phenotypes and individuals are larger, and the markers are very dense resulting in a QTL mapping with a bigger dataset.

Construction of a linkage map of the Rennell Island Tall coconut type (Cocos nucifera L.) and QTL analysis for yield characters

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 962-970 ◽  
Author(s):  
P Lebrun ◽  
L Baudouin ◽  
R Bourdeix ◽  
J Louis Konan ◽  
J HA Barker ◽  
...  
Keyword(s):  
Linkage Map ◽  
Qtl Analysis ◽  
Dna Markers ◽  
Marker Assisted Selection ◽  
Ssr Marker ◽  
Cocos Nucifera ◽  
Genome Length ◽  
Linkage Groups ◽  
Consecutive Sampling ◽  
Cocos Nucifera L

AFLP and SSR DNA markers were used to construct a linkage map in the coconut (Cocos nucifera L.; 2n = 32) type Rennell Island Tall (RIT). A total of 227 markers were arranged into 16 linkage groups. The total genome length corresponded to 1971 cM for the RIT map, with 5–23 markers per linkage group. QTL analysis for yield characters in two consecutive sampling periods identified nine loci. Three and two QTLs were detected for number of bunches and one and three QTLs for number of nuts. The correlation of trait values between characters and evaluation periods is partially reflected in identical QTLs. The QTLs represent characters that are important in coconut breeding. The cosegregation of markers with these QTLs provides an opportunity for marker-assisted selection in coconut breeding programmes.Key words: coconut, QTL, AFLP, SSR, marker-assisted selection (MAS).

scholarly journals QTL analysis of domestication syndrome in zombi pea (Vigna vexillata), an underutilized legume crop

PLoS ONE ◽  
2018 ◽  
Vol 13 (12) ◽  
pp. e0200116 ◽  
Author(s):  
Sujinna Dachapak ◽  
Norihiko Tomooka ◽  
Prakit Somta ◽  
Ken Naito ◽  
Akito Kaga ◽  
...  
Keyword(s):  
Qtl Analysis ◽  
Domestication Syndrome ◽  
Legume Crop ◽  
Vigna Vexillata ◽  
Underutilized Legume

scholarly journals Regression Based Robust QTL Analysis for F2 Population

2016 ◽  
Vol 44 ◽  
pp. 95-99
Author(s):  
Md. Jahangir Alam ◽  
Md. Alamin ◽  
Most. Humaira Sultana ◽  
Md. Amanullah ◽  
Md. Nurul Haque Mollah
Keyword(s):  
Qtl Analysis ◽  
Statistical Approach ◽  
Robust Regression ◽  
Likelihood Function ◽  
Computation Time ◽  
Interval Mapping ◽  
Tuning Parameter ◽  
F2 Population ◽  
Simulation Results ◽  
Trait Locus

This Quantitative trait locus (QTL) analysis is a widely used statistical approach for the detection of important genes in the chromosomes. Maximum likelihood (ML) based interval mapping (IM) is one of the most popular approaches for QTL analysis. However, it is relatively complex and computationally slower than regression based IM. Haley-Knott (HK) and extended Haley-Knott (eHK) regression based IM save computation time and produce similar results as ML-IM. However, these approaches are not robust against phenotypic outliers. In this research, we have developed a robust regression based IM approach by maximizing beta-likelihood function for intercross (F2) population. The proposed method reduces to the HK-IM method when beta ? 0. The tuning parameter beta controls the performance of the proposed method. The simulation results show that the proposed method improves performance over the existing IM approaches in the case of data contaminations; otherwise, it shows almost the same results as the classical IM approaches.

scholarly journals A Major and Stable Quantitative Trait Locus qSS2 for Seed Size and Shape Traits in a Soybean RIL Population

2021 ◽  
Vol 12 ◽  
Author(s):  
Giriraj Kumawat ◽  
Donghe Xu
Keyword(s):  
Quantitative Trait Locus ◽  
Seed Size ◽  
Quantitative Trait ◽  
Interval Mapping ◽  
Seed Shape ◽  
Significant Qtls ◽  
Size And Shape ◽  
Growing Seasons ◽  
Ril Population ◽  
Trait Locus

Seed size and shape traits are important determinants of seed yield and appearance quality in soybean [Glycine max (L.) Merr.]. Understanding the genetic architecture of these traits is important to enable their genetic improvement through efficient and targeted selection in soybean breeding, and for the identification of underlying causal genes. To map seed size and shape traits in soybean, a recombinant inbred line (RIL) population developed from K099 (small seed size) × Fendou 16 (large seed size), was phenotyped in three growing seasons. A genetic map of the RIL population was developed using 1,485 genotyping by random amplicon sequencing-direct (GRAS-Di) and 177 SSR markers. Quantitative trait locus (QTL) mapping was conducted by inclusive composite interval mapping. As a result, 53 significant QTLs for seed size traits and 27 significant QTLs for seed shape traits were identified. Six of these QTLs (qSW8.1, qSW16.1, qSLW2.1, qSLT2.1, qSWT1.2, and qSWT4.3) were identified with LOD scores of 3.80–14.0 and R2 of 2.36%–39.49% in at least two growing seasons. Among the above significant QTLs, 24 QTLs were grouped into 11 QTL clusters, such as, three major QTLs (qSL2.3, qSLW2.1, and qSLT2.1) were clustered into a major QTL on Chr.02, named as qSS2. The effect of qSS2 was validated in a pair of near isogenic lines, and its candidate genes (Glyma.02G269400, Glyma.02G272100, Glyma.02G274900, Glyma.02G277200, and Glyma.02G277600) were mined. The results of this study will assist in the breeding programs aiming at improvement of seed size and shape traits in soybean.

scholarly journals Construction of a Genetic Linkage Map and QTL Analysis of Fruit-related Traits in an F1 Red Fuji x Hongrou Apple Hybrid

2016 ◽  
Vol 11 (1) ◽  
pp. 487-497 ◽  
Author(s):  
Zunchun Liu ◽  
Donge Bao ◽  
Daliang Liu ◽  
Yanmin Zhang ◽  
Muhammad Aqeel Ashraf ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Linkage ◽  
Molecular Mechanisms ◽  
Genetic Linkage Map ◽  
Sugar Content ◽  
Interval Mapping ◽  
Major Effect ◽  
Fruit Weight ◽  
Soluble Solids ◽  
Linkage Groups

AbstractA genetic linkage map of the apple, composed of 175 SSR and 105 SRAP markers, has been constructed using 110 F1 individuals obtained from a cross between the ‘Red Fuji’ Malus domestica and ‘Hongrou’ Malus sieversii cultivars, which have relatively high levels of DNA marker polymorphism and differ remarkably in fruit-related traits. The linkage map comprised 17 linkage groups, covering 1299.67 cM with an average marker distance of 4.6 cM between adjacent markers, or approximately 91% of Malus genome. Linkage groups were well populated and, although marker density ranged from 2.1 to 9.5 cM, just 10 gaps of more than 15 cM were observed. Moreover, just 12.5% of markers displayed segregation distortion. The present genetic linkage map was used to identify quantitative trait loci (QTLs) affecting fruit-related traits. 23 QTLs for ten fruit traits were detected by multiple interval mapping: 3 QTLs for Vc content, One QTL for single fruit weight, 2 QTLs for peel-phenols content, 2 QTLs for flesh-hardness, 2 QTLs for diameter, 6 QTLs for acid content, 1 QTL for sugar content, 2 QTLs for soluble solids content, 2 QTLs for flesh-phenols and 2 QTLs for brittleness. These QTLs were located on linkage groups C1, C2, C3, C5, C6, C7, C9, C10, C14 and C17, respectively. The phenotypic variations exhibited by each QTL ranged from 2% to 72%, and their LOD values varied from 2.03 to 8.93, of which five QTLs were major effect genes (R2 ≥ 10%). The tight linkage markers (*me2em7-460f, *MS01a03-180m, *me1em6-307m, *CH05c06-102f, *me1em8-423f) would be helpful to elucidate the molecular mechanisms of apple domestication and breeding in the future.

scholarly journals Unconditional and Conditional Quantitative Trait Loci Mapping for Plant Height in Nonheading Chinese Cabbage

HortScience ◽  
2009 ◽  
Vol 44 (2) ◽  
pp. 268-273 ◽  
Author(s):  
Yan Cheng ◽  
Qian Wang ◽  
Qingyu Ban ◽  
Jianfeng Geng ◽  
Xiao Wei Zhang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Plant Height ◽  
Chinese Cabbage ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
Genetic Model ◽  
Interval Mapping ◽  
Genetic Effects ◽  
Linkage Groups ◽  
Trait Loci

Quantitative trait loci (QTLs) identified so far in Brassica were mainly generated in the final stage of plant development, which did not apply to the exploitation of genetic effects that were expressed during a specific developmental stage. Thus, the objective of this study was to simultaneously identify unconditional and conditional QTL associated with plant height at various stages of nonheading Chinese cabbage. One hundred twelve doubled haploid (DH) lines developed from the cross between nonheading Chinese cabbage lines ‘SW-13’ and ‘SU-124’ were used for QTL analysis of plant height by the composite interval mapping method combined with mixed genetic model. The map we used for QTL analysis was an updated version of the first genetic map of nonheading Chinese cabbage with 48 additional markers to the same DH population. With data from 2 years, a total of 11 unconditional QTLs in six linkage groups and 23 conditional QTLs in eight linkage groups were identified for plant height. The results indicated that the number and type of QTLs and their genetic effects for plant height were different in a series of measuring stages. Each QTL can explain 7.92% to 28.25% of the total phenotypic variation. Two QTLs (ph8-4 and ph8-5) were identified to be associated with plant height using both unconditional and conditional mapping methods simultaneously in 2 years. These results demonstrated that it is highly effective for mapping QTL of developmental traits using the unconditional and conditional analysis methodology.

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