High‐density SNP‐based genetic diversity and heterotic patterns of tropical maize breeding lines

Crop Science ◽  
2020 ◽  
Vol 60 (2) ◽  
pp. 779-787 ◽  
Author(s):  
Karla Jorge Silva ◽  
Claudia Teixeira Guimarães ◽  
José Henrique Soler Guilhen ◽  
Paulo Evaristo de Oliveira Guimarães ◽  
Sidney Netto Parentoni ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
High Density ◽  
Tropical Maize ◽  
Maize Breeding ◽  
Breeding Lines

scholarly journals Phenotypic and molecular characterization of a set of tropical maize inbred lines from a public breeding program in Brazil

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Sirlene Viana de Faria ◽  
Leandro Tonello Zuffo ◽  
Wemerson Mendonça Rezende ◽  
Diego Gonçalves Caixeta ◽  
Hélcio Duarte Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbred Lines ◽  
Breeding Program ◽  
Tropical Maize ◽  
Maize Breeding ◽  
Breeding Programs ◽  
The Public ◽  
Maize Inbred Lines

Abstract Background The characterization of genetic diversity and population differentiation for maize inbred lines from breeding programs is of great value in assisting breeders in maintaining and potentially increasing the rate of genetic gain. In our study, we characterized a set of 187 tropical maize inbred lines from the public breeding program of the Universidade Federal de Viçosa (UFV) in Brazil based on 18 agronomic traits and 3,083 single nucleotide polymorphisms (SNP) markers to evaluate whether this set of inbred lines represents a panel of tropical maize inbred lines for association mapping analysis and investigate the population structure and patterns of relationships among the inbred lines from UFV for better exploitation in our maize breeding program. Results Our results showed that there was large phenotypic and genotypic variation in the set of tropical maize inbred lines from the UFV maize breeding program. We also found high genetic diversity (GD = 0.34) and low pairwise kinship coefficients among the maize inbred lines (only approximately 4.00 % of the pairwise relative kinship was above 0.50) in the set of inbred lines. The LD decay distance over all ten chromosomes in the entire set of maize lines with r2 = 0.1 was 276,237 kb. Concerning the population structure, our results from the model-based STRUCTURE and principal component analysis methods distinguished the inbred lines into three subpopulations, with high consistency maintained between both results. Additionally, the clustering analysis based on phenotypic and molecular data grouped the inbred lines into 14 and 22 genetic divergence clusters, respectively. Conclusions Our results indicate that the set of tropical maize inbred lines from UFV maize breeding programs can comprise a panel of tropical maize inbred lines suitable for a genome-wide association study to dissect the variation of complex quantitative traits in maize, mainly in tropical environments. In addition, our results will be very useful for assisting us in the assignment of heterotic groups and the selection of the best parental combinations for new breeding crosses, mapping populations, mapping synthetic populations, guiding crosses that target highly heterotic and yielding hybrids, and predicting untested hybrids in the public breeding program UFV.

scholarly journals Morphological Characterization, Variability and Diversity among Vegetable Soybean (Glycine max L.) Genotypes

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 671
Author(s):  
Nagaraju Shilpashree ◽  
Sarojinikunjamma Nirmala Devi ◽  
Dalasanuru Chandregowda Manjunathagowda ◽  
Anjanappa Muddappa ◽  
Shaimaa A. M. Abdelmohsen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Improvement ◽  
Genotypic Variation ◽  
Morphological Characterization ◽  
High Yield ◽  
Vegetable Soybean ◽  
Breeding Lines ◽  
Commercial Cultivation ◽  
Soybean Genotypes ◽  
High Heritability

Vegetable soybean production is dependent on the development of vegetable type varieties that would be achieved by the use of germplasm to evolve new agronomically superior yielding vegetable type with beneficial biochemical traits. This can be accomplished by a better understanding of genetics, which is why the research was conducted to reveal the quantitative genetics of vegetable soybean genotypes. Genetic variability of main morphological traits in vegetable soybean genotypes and their divergence was estimated, as a result of the magnitude of genotypic variation (GV), and phenotypic variation (PV) of traits varied among the genotypes. All traits showed high heritability (h2) associated with high genetic advance percentage mean (GAM). Therefore, these variable traits are potential for genetic improvement of vegetable type soybean. Genetic diversity is the prime need for breeding, and the magnitude of genetic diversity values were maximized among specific genotypes. Eight clusters were found for all genotypes; cluster VIII and cluster I were considered to have the most diversity. Cluster VIII consisted of two genotypes (GM-6 and GM-27), based on the mean outcomes of the high yield attributing traits. Hence, these two (GM-6, GM-27) genotypes can be advanced for commercial cultivation; furthermore, other genotypes can be used as source of breeding lines for genetic improvement of vegetable soybean.

Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers

2021 ◽  
Vol 19 (1) ◽  
pp. 20-28
Author(s):  
Abush Tesfaye Abebe ◽  
Adesike Oladoyin Kolawole ◽  
Nnanna Unachukwu ◽  
Godfree Chigeza ◽  
Hailu Tefera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Glycine Max ◽  
Snp Markers ◽  
Fixation Index ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Breeding Lines ◽  
Soybean Germplasm ◽  
Elite Breeding Lines

AbstractSoybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (FST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.

Overt and Concealed Genetic Loads Revealed by QTL Mapping of Genotype-dependent Viability in the Pacific Oyster Crassostrea gigas

Genetics ◽  
2021 ◽  
Author(s):  
Xiaoshen Yin ◽  
Dennis Hedgecock
Keyword(s):  
Genetic Diversity ◽  
Crassostrea Gigas ◽  
Pacific Oyster ◽  
Genetic Load ◽  
High Density ◽  
High Genetic Diversity ◽  
High Fecundity ◽  
Recessive Mutations ◽  
Genotype Frequencies ◽  
The Pacific

Abstract Understanding the genetic bases of inbreeding depression, heterosis, and genetic load is integral to understanding how genetic diversity is maintained in natural populations. The Pacific oyster Crassostrea gigas, like many long-lived plants, has high fecundity and high early mortality (type-III survivorship), manifesting a large, overt, genetic load; the oyster harbors an even greater concealed genetic load revealed by inbreeding. Here, we map viability QTL (vQTL) in six interrelated F2 oyster families, using high-density linkage maps of single nucleotide polymorphisms generated by genotyping-by-sequencing (GBS) methods. Altogether, we detect 70 vQTL and provisionally infer 89 causal mutations, 11 to 20 per family. Genetic mortality caused by independent (unlinked) vQTL ranges from 94.2% to 97.8% across families, consistent with previous reports. High-density maps provide better resolution of genetic mechanisms, however. Models of one causal mutation present in both identical-by-descent (IBD) homozygotes and heterozygotes fit genotype frequencies at 37 vQTL; consistent with the mutation-selection balance theory of genetic load, 20 are highly deleterious, completely recessive mutations and 17 are less deleterious, partially dominant mutations. Another 22 vQTL require pairs of recessive or partially dominant causal mutations, half showing selection against recessive mutations linked in repulsion, producing pseudo-overdominance. Only eight vQTL appear to support the overdominance theory of genetic load, with deficiencies of both IBD homozygotes, but at least four of these are likely caused by pseudo-overdominance. Evidence for epistasis is absent. A high mutation rate, random genetic drift, and pseudo-overdominance may explain both the oyster’s extremely high genetic diversity and a high genetic load maintained primarily by mutation-selection balance.

scholarly journals Spontaneous Activation of Quiescent Uq Transposable Elements during Endosperm Development in Zea Mays.

Genetics ◽  
1988 ◽  
Vol 119 (2) ◽  
pp. 457-464
Author(s):  
Y B Pan ◽  
P A Peterson
Keyword(s):  
Transposable Elements ◽  
Normal Growth ◽  
Growth Conditions ◽  
Inbred Lines ◽  
Endosperm Development ◽  
Maize Breeding ◽  
Breeding Lines ◽  
Element System ◽  
Aleurone Tissue ◽  
Sufficient Stimulus

Abstract This study addresses the question of the activation of quiescent transposable elements in maize breeding lines. The a-ruq reporter allele of the Uq transposable element system expresses Uq activity (spots or sectors of spots in otherwise colorless aleurone tissue) when exposed to various genotypes of assorted maize inbred lines lacking any active Uq element. This activation of quiescent Uq elements occurs randomly during the growth of the endosperm. It is concluded that there are components in the genome that enhance the rare activation of quiescent Uq elements. Further, it seems that this activation occurs in the absence of any stress-inducing treatment, but that normal growth conditions provide sufficient stimulus for such activation.

Genetic Diversity among Common Bean Breeding Lines Developed for Central America

Crop Science ◽  
1995 ◽  
Vol 35 (4) ◽  
pp. 1178-1183 ◽  
Author(s):  
Stephen E. Beebe ◽  
Ivan Ochoa ◽  
Paul Skroch ◽  
James Nienhuis ◽  
Jan Tivang
Keyword(s):  
Genetic Diversity ◽  
Common Bean ◽  
Central America ◽  
Breeding Lines

scholarly journals High-density Genotyping reveals Genomic Characterization, Population Structure and Genetic Diversity of Indian Mithun (Bos frontalis)

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Anupama Mukherjee ◽  
Sabyasachi Mukherjee ◽  
Rajan Dhakal ◽  
Moonmoon Mech ◽  
Imsusosang Longkumer ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
High Density ◽  
Genomic Characterization

Genome Analysis of Mungbean [Vigna radiata (L.) Wilczek] using Simple Sequence Repeats (SSR) Mapping Data

2021 ◽  
Author(s):  
Babita Rani ◽  
Renu Singh ◽  
Minakshi Jattan ◽  
Shubham Kumar ◽  
Ram Kumar
Keyword(s):  
Genetic Diversity ◽  
Agricultural Research ◽  
Ammonium Bromide ◽  
Breeding Lines ◽  
Iron And Zinc ◽  
Zinc Concentrations ◽  
Increase Productivity ◽  
Cetyltrimethyl Ammonium ◽  
Simple Sequence

Background: Agricultural research chiefly focuses on the ways to increase productivity of staple food crops like wheat and rice, but still there are crops where research focus is meagre like nutritionally important mungbean crop grown by marginal farmers in crop rotation systems. Mungbean is leguminous crop which is high in protein content thus it offers health benefits at cheaper rates. The present work emphasizes on finding genetic diversity in mungbean germplasm on the basis of chemical and molecular analysis for micronutrients variation (iron and zinc). The identified molecular markers having linkage with high iron and zinc concentrations in the seeds can prove helpful in expansion of biofortification programme.Methods: Fifty-one green gram genotypes viz. varieties released from CCS Haryana Agricultural University (HAU), Hisar, Punjab Agricultural University (PAU), Ludhiana, Indian Institute of Pulse Research (IIPR), Kanpur and some advanced breeding lines were included in the study. Acid digested samples were used for determination of Fe and Zn by Atomic Absorption Spectrophotometer. Young seedlings leaves were used for isolation of genomic DNA using 2% CTAB (cetyltrimethyl ammonium bromide). Result: Total of fifty-one mungbean genotypes were tested using fifty simple sequence repeat (SSR) primers. Out of fifty primers screened, 16 primers generated 35 bands. Iron (Fe) and zinc (Zn) in mungbean lines was 36.90 to 107.1 mg/kg and 14.2 to 53.8 mg/kg respectively. The molecular studies based on SSR markers also indicates existence of ample genetic diversity at molecular level.

Genetic diversity and population structure of the rice false smut pathogen Ustilaginoidea virens in Sichuan-Chongqing region

Plant Disease ◽  
2021 ◽  
Author(s):  
Anfei Fang ◽  
Zhuangyuan Fu ◽  
Zexiong Wang ◽  
Yuhang Fu ◽  
Yubao Qin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variation ◽  
Genetic Recombination ◽  
Resistance Breeding ◽  
Ustilaginoidea Virens ◽  
Breeding Lines ◽  
Rice False Smut ◽  
Geographical Populations ◽  
False Smut

Rice false smut caused by Ustilaginoidea virens is currently one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from SNP-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. The groups Ⅰ and Ⅵ were the largest including 61 and 48 isolates, respectively. The pairwise FST values showed significant genetic differentiation among all compared geographical populations. AMOVA showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup. The UPGMA dendrogram and population structure revealed that the genetic composition of isolates collected from ST (Santai), NC (Nanchong), YC (Yongchuan), and WS (Wansheng) dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

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