Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs

Thirunavukkarasu, Nepolean; Hossain, Firoz; Shiriga, Kaliyugam; Mittal, Swati; Arora, Kanika; Rathore, Abhishek; Mohan, Sweta; Shah, Trushar; Sharma, R.C.; Namratha, Pottekatt Mohanlal; Mithra, Amitha S V C R; Mohapatra, Trilochan; Gupta, H. S.

doi:10.1186/1471-2164-14-877

Cited by 22 publications

(29 citation statements)

References 68 publications

(94 reference statements)

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“…In this panel, the LD decay distance ranged from 397 kb on chromosome 1 to 819 kb on chromosome 10, with an average of 643 kb. This is largely consistent with the values observed in previous studies (Thirunavukkarasu et al 2013;Wu et al 2014). In addition, the average distance between adjacent SNPs was 50 kb in this panel.…”

Section: Linkage Disequilibriumsupporting

confidence: 93%

“…Knowledge of genetic diversity can be leveraged in germplasm improvement and quantitative trait analysis (Thirunavukkarasu et al 2013). The 240 inbred lines in this study could be partitioned into five subgroups, which indicates that different kinds and unequal frequencies of alleles are distributed across these five subgroups.…”

Section: Genetic Diversitymentioning

confidence: 99%

“…Ln (the probability of data) was calculated for each K, and then delta K (Dk) was calculated for values of K from 2 to 10. With the proper value of K, each inbred line was assigned to a single subgroup with the largest membership coefficient (Q value) (Thirunavukkarasu et al 2013). NTSYSpc version 2.2 was used to produce dendrograms (Sun 2007).…”

Section: Analysis Of Population Structurementioning

confidence: 99%

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Genetic properties of 240 maize inbred lines and identity-by-descent segments revealed by high-density SNP markers

Liu

Zhang

et al. 2015

Mol Breeding

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Characterization of the genetic properties of maize inbred lines is beneficial not only for increasing knowledge of genetic diversity, but also for maize breeding. In the present study, a panel of 240 maize inbred lines commonly used in China, including three foundation parents Dan340, Mo17, and Huangzao4, and their derivatives, was genotyped using the MaizeSNP50 BeadChip, which contains 56,110 single-nucleotide polymorphism (SNP) markers. As a result, 40,757 SNPs with unique physical positions were successfully recalled in this panel with an average coverage of 50 kb per SNP. Five subgroups including Lan, LRC, PB, Reid, and SPT were inferred using 4000 SNPs with minor allele frequency C0.200, a result that was largely consistent with the pedigree information for these 240 inbred lines. With a cutoff value of r 2 \ 0.100, linkage disequilibrium (LD) decay distances along the ten chromosomes of maize ranged from 397 to 819 kb, with an average of 643 kb. A subtotal of 26, 35, and 23 identity-by-descent segments, which were longer than both the average LD decay distance on the corresponding chromosomes and the local LD decay distance of r 2 \ 0.100, were identified in the Dan340, Huangzao4, and Mo17 derivatives, respectively. Three lower peaks for Tajima's D overlapped with three major quantitative trait loci (qkrn7, scmv1, and qHS2.09) in these derivatives. Elucidating the genetic properties of this panel provides information for investigating the genetic architecture of agronomic traits and heterotic grouping during maize breeding.

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Section: Linkage Disequilibriumsupporting

confidence: 93%

Section: Genetic Diversitymentioning

confidence: 99%

Section: Analysis Of Population Structurementioning

confidence: 99%

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Genetic properties of 240 maize inbred lines and identity-by-descent segments revealed by high-density SNP markers

Liu

Zhang

et al. 2015

Mol Breeding

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“…We performed a Principal Component Analysis (PCA) following the procedure as reported 19 . The eigenvector decomposition of the genotype data was performed by the eigen function in R. The whole program was provided by the SNPrelate package in R 20 .…”

Section: Methodsmentioning

confidence: 99%

Draft genome sequence of an eliteDurapalm and whole-genome patterns of DNA variation in oil palm

Jin

Lee

Bai

et al. 2016

DNA Res

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Oil palm is the world’s leading source of vegetable oil and fat. Dura, Pisifera and Tenera are three forms of oil palm. The genome sequence of Pisifera is available whereas the Dura form has not been sequenced yet. We sequenced the genome of one elite Dura palm, and re-sequenced 17 palm genomes. The assemble genome sequence of the elite Dura tree contained 10,971 scaffolds and was 1.701 Gb in length, covering 94.49% of the oil palm genome. 36,105 genes were predicted. Re-sequencing of 17 additional palm trees identified 18.1 million SNPs. We found high genetic variation among palms from different geographical regions, but lower variation among Southeast Asian Dura and Pisifera palms. We mapped 10,000 SNPs on the linkage map of oil palm. In addition, high linkage disequilibrium (LD) was detected in the oil palms used in breeding populations of Southeast Asia, suggesting that LD mapping is likely to be practical in this important oil crop. Our data provide a valuable resource for accelerating genetic improvement and studying the mechanism underlying phenotypic variations of important oil palm traits.

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“…Higher LD and slower LD decay was observed in biparental and multiparental maize populations [9]. The number and length of haplotype blocks is also highly variable [4,7].…”

mentioning

confidence: 95%

Linkage disequilibrium and haplotype block patterns in popcorn populations

Andrade

Viana

Pereira

et al. 2019

Preprint

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Linkage disequilibrium (LD) analysis provides information on evolutionary aspects of the 9 populations and allows selecting populations and single nucleotide polymorphisms (SNPs) for 10 association studies. Recently, haplotype blocks have been used to increase the power of quantitative 11 trait loci detection in genome-wide association studies and the prediction accuracy with genomic 12 selection. The objectives of this study were to compare the degree of LD, the LD decay, the LD 13 decay extent, and the number and length of haplotype blocks in the populations and to elaborate the 14 first LD map for maize, for elucidating if the maize chromosomes also had a pattern of interspaced 15 regions of high and low rates of recombination. We used a biparental temperate population, a 16 tropical synthetic, and a tropical breeding population, genotyped for approximately 75,000 SNPs. 17The level of LD expressed by the r 2 values is surprisingly low (0.02, 0.04, and 0.04), but 18 comparable to some non-isolated human populations. The general evidence is that the synthetic is 19 the population with higher LD. It is not expected a significant advantage of haplotype-based 20 association study and along generations genomic selection due to the reduced number of SNPs in 21 the haplotype blocks (2 to 3). The results concerning LD decay (rapid decay after 5-10 kb) and LD 22 decay extent (along up to 300 kb) are in the range observed with maize inbred line panels. Our most 23 important result is that maize chromosomes had a pattern of regions of extensive LD interspaced 24 with regions of low LD. However, our simple simulated LD map provides evidence that this pattern 25 can reflect regions with differences of allele frequencies and LD level (expressed by D') and not 26 regions with high and low rates of recombination. 27 Keywords: gametic phase disequilibrium; LD map; haplotype blocks; intragenic LD. Introduction Linkage disequilibrium (LD) analysis is important to humans, other animal species, and plants because the results can be used for positional cloning, provide information on rate of recombination, gene conversion, and evolutionary aspects of the populations, including recombination history, mutation, selection, genetic drift, and admixture, and allows selecting populations and single nucleotide polymorphisms (SNPs) for association studies [1]. The most common LD measures are D' and r 2 . The statistic D' is the ratio between D (the difference between products of haplotypes, D = P(AB).P(ab)  P(Ab).P(aB)) and the deviation of the actual gametic frequency from linkage equilibrium [2]. The statistic r 2 is the square of the correlation between the values of alleles at two loci in the same gamete, where D is the covariance [3]. Additional information on historical recombination is provided by the analysis of the haplotype blocks pattern in populations. A haplotype block is a chromosome region in which there are few haplotypes (combinations of alleles of multiple SNPs within a haplotype block) (2-4 per block), and for which the ...

show abstract

Unraveling the genetic architecture of subtropical maize (Zea mays L.) lines to assess their utility in breeding programs

Cited by 22 publications

References 68 publications

Genetic properties of 240 maize inbred lines and identity-by-descent segments revealed by high-density SNP markers

Genetic properties of 240 maize inbred lines and identity-by-descent segments revealed by high-density SNP markers

Draft genome sequence of an eliteDurapalm and whole-genome patterns of DNA variation in oil palm

Linkage disequilibrium and haplotype block patterns in popcorn populations

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