Genetic diversity and heterotic grouping of sorghum lines using SNP markers

Sorghum breeding programs are based predominantly on developing homozygous lines to produce single cross hybrids, frequently with relatively narrow genetic bases. The adoption of complementary strategies, such as genetic diversity study, enables a broader vision of the genetic structure of the breeding germplasm. The purpose of this study was to evaluate the genetic diversity of sorghum breeding lines using structure analysis, principal components (PC) and clustering analyses. A total of 160 sorghum lines were genotyped with 29,649 SNP markers generated by genotyping-by-sequencing (GBS). The PC and clustering analyses consistently divided the R (restorer) and B (maintainer) lines based on their pedigree, generating four groups. Thirty-two B and 21 R lines were used to generate 121 single-cross hybrids, whose performances were compared based on the diversity clustering of each parental line. The genetic divergence of B and R lines indicated a potential for increasing heterotic response in the development of hybrids. The genetic distance was correlated to heterosis, allowing for the use of markers to create heterotic groups in sorghum.

Keywords:
Sorghum bicolor; Principal components; restorer; maintainer; heterosis; hybrid parents

Authorship

Karla Jorge da Silva

Universidade Federal de Viçosa – Depto. de Biologia Geral, Av. Peter Henry Rolfs, s/n, Campus Universitário – 36570-900 – Viçosa, MG – Brasil.Universidade Federal de ViçosaBrasilViçosa, MG, BrasilUniversidade Federal de Viçosa – Depto. de Biologia Geral, Av. Peter Henry Rolfs, s/n, Campus Universitário – 36570-900 – Viçosa, MG – Brasil.

http://orcid.org/0000-0002-6069-0619

Maria Marta Pastina

Embrapa Milho e Sorgo, Rod. MG-424, km 45 – 35701-970 – Sete Lagoas, MG – Brasil.Embrapa Milho e SorgoBrasilSete Lagoas, MG, BrasilEmbrapa Milho e Sorgo, Rod. MG-424, km 45 – 35701-970 – Sete Lagoas, MG – Brasil.

http://orcid.org/0000-0002-9112-3457

Claudia Teixeira Guimarães

http://orcid.org/0000-0002-4406-4968

Jurandir Vieira Magalhães

http://orcid.org/0000-0002-6673-6497

Leonardo Duarte Pimentel

Universidade Federal de Viçosa/CCA – Depto. de Fitotecnia – Viçosa, MG – Brasil.Universidade Federal de ViçosaBrasilViçosa, MG, BrasilUniversidade Federal de Viçosa/CCA – Depto. de Fitotecnia – Viçosa, MG – Brasil.

http://orcid.org/0000-0003-2620-4039

Robert Eugene Schaffert

http://orcid.org/0000-0002-9388-8031

Marcos de Oliveira Pinto

http://orcid.org/0000-0001-8117-4077

Vander Fillipe de Souza

FT Sementes, Av. Newton Slaviero, 2602 – 84043-560 – Ponta Grossa, PR – Brasil.FT SementesBrasilPonta Grossa, PR, BrasilFT Sementes, Av. Newton Slaviero, 2602 – 84043-560 – Ponta Grossa, PR – Brasil.

http://orcid.org/0000-0003-0329-7877

Karine da Costa Bernardino

http://orcid.org/0000-0002-0027-4218

Michele Jorge da Silva

http://orcid.org/0000-0001-8648-8825

Aluízio Borém

http://orcid.org/0000-0003-1386-5903

Cicero Beserra de Menezes ^** Corresponding author < cicero.menezes@embrapa.br >

http://orcid.org/0000-0001-9437-6946

* Corresponding author < cicero.menezes@embrapa.br >

Edited by: Alencar Xavier

Authors' Contributions

Conceptualization: Silva, K.J.; Guimarães, C.T.; Magalhães, J.V.; Pimentel, L.D.; Schaffert, R.E.; Borém, A.; Menezes, C.B. Data acquisition: Guimarães, C.T.; Magalhães, J.V.; Pastina, M.M; Souza, V.F.; Menezes, C.B.; Pinto, M.O. Data analysis: Silva, K.J.; Pastina, M.M.; Souza, V.F.; Bernardino, K.C.; Silva, M.J.; Magalhães, J.V.; Guimarães, C.T.; Design of methodology: Guimarães, C.T.; Magalhães, J.V.; Pimentel, L.D; Pastina, M.M; Souza, V.F.; Menezes, C.B. Writing and editing: Silva, K.J.; Guimarães, C.T.; Magalhães, J.V.; Schaffert, R.E.; Menezes, C.B.; Pastina, M.M; Bernardino, K.C.

SCIMAGO INSTITUTIONS RANKINGS

Figures | Formulas

Figures (6)
Formulas (3)

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Figure 1
A – Values of ΔK for each k, calculated according to Evanno et al. (2005)Evanno, G.; Regnaut. S.; Goudet. J. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14: 2611–2620. for 10 simulations in the Structure program (k = 2). B – The bars with values plotted on the x-axis correspond to the genome of each individual belonging to one of the two subpopulations: blue (109 restorer lines) and red (51 maintainer lines).

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Figure 2
PCA analysis based on 29,649 SNP markers for 160 sorghum lines. The two first principal components (PC) divided the lines into four groups: G1 = Lines derived from BRP5BR, SC748, SC326; G2 = Lines derived from BRP5BR, BRP3BR, SC326, TX2536, SC170; G3 = Lines derived from SC748, SC326, SC170; G4 = Lines derived from ATF54, ARG1, TX623.

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Figure 3
Cluster of the 160 lines evaluated according to the Neighbor-Joining method, considering the data of 29,649 SNPs markers. Genetic distances between sorghum lines were calculated using the identity-by-state (IBS) coefficient. The colors inside the branches followed the same as those obtained by using the two first principal components.

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Figure 4
Heatmap of pairwise relative values Individuals (IBS matrix) and dendrogram based on 86,342 SNPs among. The color histogram shows the distribution of coefficients of coancestry values in the whole matrix, the stronger the red zones, the more individuals will be related to each other. Colors represent the genetic diversity groups identified through the Neighbor-Joining method.

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Figure 5
The correlation between genetic distance of the parents, Heterosis, Heterolbeltiosis and Grain Yield. The phenotypic data was consisted of 121 hybrids between 32 maintainer lines and 21 restorer lines.

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Figure 6
Boxplots of the principal component analysis (PCA) based on 29.649 SNPs markers for 121 hybrids, according to heterosis (H %), heterobeltiosis (BPH %) and grain yield (GY). Number of hybrids per crosses: 1 × 2 (7 hybrids), 1 × 3 (30 hybrids), 1 × 4 (22 hybrids), 2 × 3 (13 hybrids), 2 × 4 (12 hybrids), 3 × 3 (14 hybrids), 3 × 4 (20 hybrids).

Thumbnail

Figure 1 A – Values of ΔK for each k, calculated according to Evanno et al. (2005)Evanno, G.; Regnaut. S.; Goudet. J. 2005. Detecting the number of clusters of individuals using the software structure: a simulation study. Molecular Ecology 14: 2611–2620. for 10 simulations in the Structure program (k = 2). B – The bars with values plotted on the x-axis correspond to the genome of each individual belonging to one of the two subpopulations: blue (109 restorer lines) and red (51 maintainer lines).

Figure 2 PCA analysis based on 29,649 SNP markers for 160 sorghum lines. The two first principal components (PC) divided the lines into four groups: G1 = Lines derived from BRP5BR, SC748, SC326; G2 = Lines derived from BRP5BR, BRP3BR, SC326, TX2536, SC170; G3 = Lines derived from SC748, SC326, SC170; G4 = Lines derived from ATF54, ARG1, TX623.

Figure 3 Cluster of the 160 lines evaluated according to the Neighbor-Joining method, considering the data of 29,649 SNPs markers. Genetic distances between sorghum lines were calculated using the identity-by-state (IBS) coefficient. The colors inside the branches followed the same as those obtained by using the two first principal components.

Figure 4 Heatmap of pairwise relative values Individuals (IBS matrix) and dendrogram based on 86,342 SNPs among. The color histogram shows the distribution of coefficients of coancestry values in the whole matrix, the stronger the red zones, the more individuals will be related to each other. Colors represent the genetic diversity groups identified through the Neighbor-Joining method.

Figure 5 The correlation between genetic distance of the parents, Heterosis, Heterolbeltiosis and Grain Yield. The phenotypic data was consisted of 121 hybrids between 32 maintainer lines and 21 restorer lines.

Figure 6 Boxplots of the principal component analysis (PCA) based on 29.649 SNPs markers for 121 hybrids, according to heterosis (H %), heterobeltiosis (BPH %) and grain yield (GY). Number of hybrids per crosses: 1 × 2 (7 hybrids), 1 × 3 (30 hybrids), 1 × 4 (22 hybrids), 2 × 3 (13 hybrids), 2 × 4 (12 hybrids), 3 × 3 (14 hybrids), 3 × 4 (20 hybrids).

P I C = 1 - (\sum_{i = 1}^{l} p_{i}^{2} + \sum_{i = 1}^{l - 1} \sum_{j = i + 1}^{l} 2 p_{i}^{2} p_{j}^{2}),

Y = μ + g_{i} + b_{j} + r_{k} + t_{l} + \in

Y = μ + g_{i} + r_{j} + t_{l} + L R_{m} + L B_{n} + g_{i l} + L R_{m l} + L B_{n l} + \in

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Genetic diversity and heterotic grouping of sorghum lines using SNP markers

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[1] * Corresponding author < cicero.menezes@embrapa.br >