Evaluation of SRAP marker efficiency in identifying the relationship between genetic diversities of corn inbred lines with seed quantity and quality in derived hybrids

Sharareh Fareghi; Agha Fakhr Mirlohi; Ghodratollah Saeidi; Hassan Khamisabadi

doi:10.14715/cmb/2019.65.4.2

Issue

Vol. 65 No. 4: Issue 4

Issue Published : May 12, 2019

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Evaluation of SRAP marker efficiency in identifying the relationship between genetic diversities of corn inbred lines with seed quantity and quality in derived hybrids

https://doi.org/10.14715/cmb/2019.65.4.2

Sharareh Fareghi

Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran

Agha Fakhr Mirlohi

Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran

Ghodratollah Saeidi

Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, Iran

Hassan Khamisabadi

Animal Science Department, Kermanshah Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Iran

Corresponding Author(s) : Sharareh Fareghi

Fareghi.sh@gmail.com

Cellular and Molecular Biology, Vol. 65 No. 4: Issue 4
Article Published : April 30, 2019

Abstract

In order to estimate the efficiency of SRAP markers for identifying the performance of seed quantity and quality in maize single crosses, 13 inbred lines obtained from CIMMYT germplasm bank were crossed to A679, K166B, K18 and MO17 testers using the lineí—tester method. The inbred lines and derived hybrids were evaluated in two experiments separately in a randomized complete block design with three replications during two growing seasons in 2014 and 2015. In order to evaluate genetic variation in the inbred lines, 25 SRAP markers were also used. The results of variance analysis between inbred lines were showed a significant variation (Pâ‰¤0.01) for seed quantity and quality. The analysis of variance among the hybrids derived from inbred lines was showed a significant variation (Pâ‰¤0.01) for oil percent, starch content, protein content, seed yield and thousand seed weights and a significant variation for the dry matter (Pâ‰¤0.05). The maximum Euclidian distance between the two lines was 24.5 times greater than the minimum distance between two lines. The PCR amplification for the 17 parentallines with the 25 combinations of SRAP primers generated a total of 205 clear and scorable bands, of which 135 were polymorphic (65.75%). The average distance between the studied lines was 0.324 on the bases of the Jaccard coefficient and maximum distance between two lines was 2.87 times greater than the minimum distance between two lines. The M1E1, M1E5, M5E3, M5E4, and M5E5 were superior to other primer combinations in expressing genetic diversity based on the primer information indices. The banding pattern of the studied primer combinations related to the genetic variation of the inbred lines based on the studied traits revealed that the M5E1 primer pair can predict the distance of inbred lines for dry matter better than other primers. Also, the primers combination of M4E4 for protein percentage, M4E4 for starch percentage, M2E3 for crude fiber, M4E3 for oil percentage, M2E5, M4E1 and M5E1 for thousand seed weight and M3E1 for seed yield, can be introduced as informative primer combination, to estimate genetic distance determination of inbred lines based on these traits. Due to the relationship between inbred lines variation based on primers combinations with the traits in hybrids progenies showed that the M2E1, M2E2, M4E1 and M5E3 for dry matter and M2E4 for starch percentage have the ability to detect hybrid performance for these traits. For traits, protein percentage, crude fiber and oil percent no suitable primers combination were found. Also, for the seed yield, three primer combinations of M1E5, M2E2 and M3E2 had the highest negative correlation. Therefore, the hybrids derived from the inbred lines with high genetic distance based on these primers combinations will have a low seed yield. The M1E2, M2E3 and M5E5 can be introduced to identify the prediction of higher thousand seed weight.

Keywords

Corn SRAP marker Efficiency Seed quality Yield.

Fareghi, S., Mirlohi, A. F., Saeidi, G., & Khamisabadi, H. (2019). Evaluation of SRAP marker efficiency in identifying the relationship between genetic diversities of corn inbred lines with seed quantity and quality in derived hybrids. Cellular and Molecular Biology, 65(4), 6–14. https://doi.org/10.14715/cmb/2019.65.4.2

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References

Govindaraj M, Vetriventhan M, Srinivasan M. Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genet Res Int, 2015; 1–14.
Fu YB. Understanding crop genetic diversity under modern plant breeding. Theor Appl Genet, 2015; 128 (11): 2131–2142.
Geleta LF, Labuschagne MT, Viljoen CD. Relationship between heterosis and genetic distance based on morphological traits and AFLP markers in pepper. Plant Breed, 2004; 123:467-473.
Fufa H, Baenziger PS, Beecher BS, Dweikat I, Graybosch RA Eskridge KM. Comparison of phenotypic and molecular marker-based classifications of hard red winter wheat cultivars. Euphytica, 2005; 145: 133–146.
Mahmoud AM, Abdel-Fatah BE. Analysis of genetic diversity among sunflower genotypes using agro-morphological traits and molecular markers. Aust J Basic Appl Sci, 2012; 6(13): 419-432.
Achar D, Awati MG, Udayakumar M, Prasad TG. Identification of putative molecular markers associated with root traits in Coffea canephora Pierre ex Froehner. Mol Biol Int, 2015; 1-11.
Aneja B, Yadav NR, Chawla V, Yadav RC. Sequence-related amplified polymorphism (SRAP) molecular marker system and its applications in crop improvement. Mol Breed, 2012; 30(4): 1635–1648.
Kesawat MS, Das BK, Molecular markers: It's application in crop improvement. J Crop Sci Biotech, 2009; 12 (4): 168 – 178.
Li G, Quiros CF. Sequence-related amplified polymorphism (SRAP), "Ža new marker system based on a simple PCR reaction: its application to mapping and gene "Žtagging in Brassica. Theor Appl Genet, 2001; 103 (2): 455-461.
Zheng HQ, Duan HJ, Hu DH, Li Y, Hao YB. Genotypic variation of Cunninghamial anceolata revealed by phenotypic traits and SRAP markers. Dendrobiology, 2015; 74: 85–94.
Dehuo H, Yan S, Shujuan W, Jiezhen W, Runhui W, Shu Y, Ruping W, Huiquan Z. Association of SRAP markers with juvenile wood basic density and growth traits in Unninghamia lanceolata (Lamb.) Dendrobiology, 2018; 79: 111–118.
Hoecker N, Keller B, Muthreich N, Chollet D, Descombes P, Piepho HP, Hochholdinger F. Comparison of maize (Zea mays L.) F1-hybrid and parental inbred line primary root transcriptomes suggests organ-specific patterns of non additive gene expression and conserved expression trends. Genetics, 2008; 179(3): 1275–1283.
Murray MG,Thompson W F. "Ž Rapid isolation of high molecular weight plant "ŽDNA. Nucleic Acids Res, 1980; 8(19): 4321-4325."Ž
Pelaez-Anderica E, Rey F, Lopez M, Gil J. Genetic diversity and phylogenetic relationships of a potential cotton collection for European breeding research. Turk J Bot, 2018; 42: 172-182.
Bertan I, De Carvalho FIF, Costa de Oliveira A. Parental Selection Strategies in Plant Breeding Programs J Crop Sci Biotech, 2007; 10 (4): 211 – 222.
Lado B, Battenfield S, Guzman C, Quincke M, Singh RP, Dreisigacker S, Gutierrez L. Strategies for selecting crosses using genomic prediction in two wheat breeding programs. Plant Genome, 2017; 10(2): 1-12.
Ertiro BT, Zeleke H, Friesen D, Blummel M, Twumasi-Afriyie S. Relationship between the performance of parental inbred lines and hybrids for food-feed traits in maize (Zea mays L.) in Ethiopia. Field Crop Res, 2013; 153: 86–93.
Basal H, Turgut I, Heterosis and combining ability for yield components and fiber quality parameters in a half diallel Cotton (G. hirsutum L.) population. Turk J Agr Forest, 2003; 27(4): 207-212.
Akhtar N, Chowdhry M. Genetic analysis of yield and some other quantitative traits in bread wheat. Int J Agric Biol, 2006; 8(4): 523-527.
Ramanatha Rao V, Hodgkin TP. Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult, 2002; 68 (1): 1–19.
Moradkhani H, Mehrabi AA, Etminan A, Pour-Aboughadareh A. Molecular diversity and phylogeny of Triticum-Aegilopsspecies possessing D genome revealed by SSR and ISSR markers. Plant Breeding and Seed Sci, 2015; 71: 81-95.
Lanza LLB, De Souza JRCL, Ottoboni LMM, Vieira MLC, De Souza AP. Genetic distance of inbred lines and prediction of maize single-cross performance using RAPD markers. Theor Appl Genet, 1997; 94: 1023-1030.
Benchimol LL, De Souza JRCL, Garcia AAF, Kono PMS, Mangolin CA, Barbosa AMM, De Souza AP. Genetic diversity in tropical maize inbred lines: heterotic group assignment and hybrid performance determined by RFLP markers. Plant Breed, 2000; 119(6): 491–496.
Karuri HW, Ateka EM, Amata RAB, Nyende AB, Muigai AWT, Mwasame E, Gichuki ST. Evaluating diversity among kenyan sweet potato genotypes using morphological and SSR markers. Int J Agric Biol, 2010; 12(1):33–38.
Ouji A, El-Bo S, Syed NH, Flavell AJ, Rouaissi M, Benyounes M, El- Gazzah M, Kharrat M. A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations. Agri Biotech, 2016; 27(8): 1513-1518.
Wu Z, Wei Ning W, Yaosheng Wang Y, Lv S, Zhao Y, Zhao X. Genetic diversity of taraxacum germplasm revealed by sequence-related amplified polymorphism (SRAP) analysis. Afr J Biotechnol, 2011; 10 (47): 9557-9562.
Francis CA. Photoperiod sensitivity and adaptation in maize. In proceeding of the 27th annual corn and sorghum research conference, Wilkinson, D.(ed.), 12-14 Dec.1972, Chicago pp. 119-131.
Ndhlela T, Herselman L, Semagn K, Magorokosho C, Mutimaamba C, Labuschagne MT. Relationships between heterosis, genetic distances and specific combining ability among CIMMYT and Zimbabwe developed maize inbred lines under stress and optimal conditions. Euphytica, 2015; 204 (3): 635–647.
Srdic J, Mladenovic Drinic S, Pajic Z, Filipovic M. Characterisation of maize inbred lines based on molecular markers, heterosis and pedigree data. Genetika, 2007; 39 (3): 355 -363.
Fernandes EH, Schuster I, Scapim CA, Vieira ESN, Coan MMD. Genetic diversity in elite inbred lines of maize and its association with heterosis. Genet Mol Res, 2015; 14 (2): 6509-6517.

References

Govindaraj M, Vetriventhan M, Srinivasan M. Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genet Res Int, 2015; 1–14.

Fu YB. Understanding crop genetic diversity under modern plant breeding. Theor Appl Genet, 2015; 128 (11): 2131–2142.

Geleta LF, Labuschagne MT, Viljoen CD. Relationship between heterosis and genetic distance based on morphological traits and AFLP markers in pepper. Plant Breed, 2004; 123:467-473.

Fufa H, Baenziger PS, Beecher BS, Dweikat I, Graybosch RA Eskridge KM. Comparison of phenotypic and molecular marker-based classifications of hard red winter wheat cultivars. Euphytica, 2005; 145: 133–146.

Mahmoud AM, Abdel-Fatah BE. Analysis of genetic diversity among sunflower genotypes using agro-morphological traits and molecular markers. Aust J Basic Appl Sci, 2012; 6(13): 419-432.

Achar D, Awati MG, Udayakumar M, Prasad TG. Identification of putative molecular markers associated with root traits in Coffea canephora Pierre ex Froehner. Mol Biol Int, 2015; 1-11.

Aneja B, Yadav NR, Chawla V, Yadav RC. Sequence-related amplified polymorphism (SRAP) molecular marker system and its applications in crop improvement. Mol Breed, 2012; 30(4): 1635–1648.

Kesawat MS, Das BK, Molecular markers: It's application in crop improvement. J Crop Sci Biotech, 2009; 12 (4): 168 – 178.

Li G, Quiros CF. Sequence-related amplified polymorphism (SRAP), "Ža new marker system based on a simple PCR reaction: its application to mapping and gene "Žtagging in Brassica. Theor Appl Genet, 2001; 103 (2): 455-461.

Zheng HQ, Duan HJ, Hu DH, Li Y, Hao YB. Genotypic variation of Cunninghamial anceolata revealed by phenotypic traits and SRAP markers. Dendrobiology, 2015; 74: 85–94.

Dehuo H, Yan S, Shujuan W, Jiezhen W, Runhui W, Shu Y, Ruping W, Huiquan Z. Association of SRAP markers with juvenile wood basic density and growth traits in Unninghamia lanceolata (Lamb.) Dendrobiology, 2018; 79: 111–118.

Hoecker N, Keller B, Muthreich N, Chollet D, Descombes P, Piepho HP, Hochholdinger F. Comparison of maize (Zea mays L.) F1-hybrid and parental inbred line primary root transcriptomes suggests organ-specific patterns of non additive gene expression and conserved expression trends. Genetics, 2008; 179(3): 1275–1283.

Murray MG,Thompson W F. "Ž Rapid isolation of high molecular weight plant "ŽDNA. Nucleic Acids Res, 1980; 8(19): 4321-4325."Ž

Pelaez-Anderica E, Rey F, Lopez M, Gil J. Genetic diversity and phylogenetic relationships of a potential cotton collection for European breeding research. Turk J Bot, 2018; 42: 172-182.

Bertan I, De Carvalho FIF, Costa de Oliveira A. Parental Selection Strategies in Plant Breeding Programs J Crop Sci Biotech, 2007; 10 (4): 211 – 222.

Lado B, Battenfield S, Guzman C, Quincke M, Singh RP, Dreisigacker S, Gutierrez L. Strategies for selecting crosses using genomic prediction in two wheat breeding programs. Plant Genome, 2017; 10(2): 1-12.

Ertiro BT, Zeleke H, Friesen D, Blummel M, Twumasi-Afriyie S. Relationship between the performance of parental inbred lines and hybrids for food-feed traits in maize (Zea mays L.) in Ethiopia. Field Crop Res, 2013; 153: 86–93.

Basal H, Turgut I, Heterosis and combining ability for yield components and fiber quality parameters in a half diallel Cotton (G. hirsutum L.) population. Turk J Agr Forest, 2003; 27(4): 207-212.

Akhtar N, Chowdhry M. Genetic analysis of yield and some other quantitative traits in bread wheat. Int J Agric Biol, 2006; 8(4): 523-527.

Ramanatha Rao V, Hodgkin TP. Genetic diversity and conservation and utilization of plant genetic resources. Plant Cell Tissue Organ Cult, 2002; 68 (1): 1–19.

Moradkhani H, Mehrabi AA, Etminan A, Pour-Aboughadareh A. Molecular diversity and phylogeny of Triticum-Aegilopsspecies possessing D genome revealed by SSR and ISSR markers. Plant Breeding and Seed Sci, 2015; 71: 81-95.

Lanza LLB, De Souza JRCL, Ottoboni LMM, Vieira MLC, De Souza AP. Genetic distance of inbred lines and prediction of maize single-cross performance using RAPD markers. Theor Appl Genet, 1997; 94: 1023-1030.

Benchimol LL, De Souza JRCL, Garcia AAF, Kono PMS, Mangolin CA, Barbosa AMM, De Souza AP. Genetic diversity in tropical maize inbred lines: heterotic group assignment and hybrid performance determined by RFLP markers. Plant Breed, 2000; 119(6): 491–496.

Karuri HW, Ateka EM, Amata RAB, Nyende AB, Muigai AWT, Mwasame E, Gichuki ST. Evaluating diversity among kenyan sweet potato genotypes using morphological and SSR markers. Int J Agric Biol, 2010; 12(1):33–38.

Ouji A, El-Bo S, Syed NH, Flavell AJ, Rouaissi M, Benyounes M, El- Gazzah M, Kharrat M. A comparative study between molecular and agro-morphological methods for describing genetic relationships in Tunisian faba bean populations. Agri Biotech, 2016; 27(8): 1513-1518.

Wu Z, Wei Ning W, Yaosheng Wang Y, Lv S, Zhao Y, Zhao X. Genetic diversity of taraxacum germplasm revealed by sequence-related amplified polymorphism (SRAP) analysis. Afr J Biotechnol, 2011; 10 (47): 9557-9562.

Francis CA. Photoperiod sensitivity and adaptation in maize. In proceeding of the 27th annual corn and sorghum research conference, Wilkinson, D.(ed.), 12-14 Dec.1972, Chicago pp. 119-131.

Ndhlela T, Herselman L, Semagn K, Magorokosho C, Mutimaamba C, Labuschagne MT. Relationships between heterosis, genetic distances and specific combining ability among CIMMYT and Zimbabwe developed maize inbred lines under stress and optimal conditions. Euphytica, 2015; 204 (3): 635–647.

Srdic J, Mladenovic Drinic S, Pajic Z, Filipovic M. Characterisation of maize inbred lines based on molecular markers, heterosis and pedigree data. Genetika, 2007; 39 (3): 355 -363.

Fernandes EH, Schuster I, Scapim CA, Vieira ESN, Coan MMD. Genetic diversity in elite inbred lines of maize and its association with heterosis. Genet Mol Res, 2015; 14 (2): 6509-6517.

Author biographies is not available.