Assessment of genetic diversity among low-nitrogen-tolerant early generation maize inbred lines using SNP markers

Ajala, S. O.; Olayiwola, M. O.; Ilesanmi, Oluyinka; Getachew, Melaku; Job, Anthony Oluwatoyosi; Olaniyan, Amudalat Bolanle

doi:10.1080/02571862.2018.1537010

Cited by 17 publications

(15 citation statements)

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“…We found all markers moderately or low informative as PIC value for all markers was less than 0.5 [34]. Other researchers also found similar results in flax [35], winter wheat [36,37], rice [38] and maize [39]. Bi-allelic nature of SNP marker and probably low mutation rate [40] restrict the PIC value within 0.5.…”

Section: Discussionsupporting

confidence: 68%

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

2020

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Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6200 SNP markers. Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise F st comparison revealed a great degree of divergence ( F st > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r = 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree and kinship matrix assist to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.

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Section: Discussionsupporting

confidence: 68%

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

2020

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“…We found all markers moderately or low informative as PIC value for all markers was less than 0.5 (35). Other researchers also found similar results in ax (36), winter wheat (37,38), rice (39) and maize (40). Bi-allelic nature of SNP marker and probably low mutation rate (41) restrict the PIC value within 0.5.…”

Section: Discussionsupporting

confidence: 58%

Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

Hoque

Fiedler

Rahman

2020

Preprint

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Abstract Background A sustainable breeding program requires a minimum level of germplasm diversity to provide varied options for the selection of new breeding lines. To maximize genetic gain of the North Dakota State University (NDSU) flax breeding program, we aimed to increase the genetic diversity of its parental stocks by incorporating diverse genotypes. For this purpose, we analyzed the genetic diversity, linkage disequilibrium, and population sub-structure of 350 globally-distributed flax genotypes with 6,200 SNP markers Results All the genotypes tested clustered into seven sub-populations (P1 to P7) based on the admixture model and the output of neighbor-joining (NJ) tree analysis and principal coordinate analysis were in line with that of structure analysis. The largest sub-population separation arose from a cluster of NDSU/American genotypes with Turkish and Asian genotypes. All sub-populations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise F st comparison revealed a great degree of divergence ( F st > 0.25) between most of the combinations. A whole collection mantel test showed significant positive correlation (r = 0.30 and p < 0.01) between genetic and geographic distances, whereas it was non-significant for all sub-populations except P4 and P5 (r= 0.251, 0.349 respectively and p < 0.05). In the entire collection, the mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 21 kb distance. Conclusions To maximize genetic gain, hybridization between NDSU stock (P5) and Asian individuals (P6) are potentially the best option as genetic differentiation between them is highest ( F st > 0.50). In contrast, low genetic differentiation between P5 and P2 may enhance the accumulation of favorable alleles for oil and fiber upon crossing to develop dual purpose varieties. As each sub-population consists of many genotypes, a Neighbor-Joining tree assists to identify distantly related genotypes. These results also inform genotyping decisions for future association mapping studies to ensure the identification of a sufficient number of molecular markers to tag all linkage blocks.

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“…Assessing genetic diversity without detailed combining ability studies and per se performance evaluations of the inbred lines limits the usefulness of the assessed lines as potential parents of hybrids and synthetics (Ajala et al., 2019). The inbred testers used in this study, INB1368 and INB9071, represent contrasting heterotic groups (Agbaje et al., 2008; Kim et al., 1999) and this was confirmed by the differences in the GCA effects due to testers for grain yield and other agronomic traits.…”

Section: Discussionmentioning

confidence: 99%

“…Eight‐hundred ul of freshly prepared modified CTAB extraction buffer (200 mM Tris, pH 7.5; 50 mM EDTA, pH 8.0; 2 M NaCl; 2% CTAB; 1% beta‐mercaptoethanol) was added to the ground powder in a 1.5 ml extraction tube and incubated at 65°C in a water bath for 30 min with continuous gentle rocking as earlier described by Ajala et al. (2019). The quality of the DNA for genotyping by sequencing (GBS) was ascertained by digesting the DNA with restriction enzyme Hin dIII and samples were sent to Genomic Diversity Facility at Cornell University for GBS.…”

Section: Methodsmentioning

confidence: 99%

Assessment of heterotic patterns of tropical low‐nitrogen–tolerant maize (Zea maysL.) inbred lines using testcross performance, morphological traits and SNP markers

et al. 2020

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Low soil fertility (Low-N) affects maize productivity in the moist savannas, a region considered the most productive for maize in West and Central Africa (Badu-Apraku et al., 2015). Fertilizer use in Africa is low with an average of 8 kg/ha (Heisey, Norton, Evenson, & Pingali, 2007; IFDC, 2006). In Nigeria, for example, less than 3.3 kg of nitrogen fertilizers are applied per hectare (FAO, 2015). Nitrogen is the most important nutrient element and the second most limiting factor for plant growth after water (Muurinen, 2007). Wolfe, Henderson, Hsiao, and Alvio (1988) and Meseka, Menkir, Ibrahim, and Ajala (2006) reported that yield losses due to low-N could be up to 50%. Low soil fertility is common in farmers' fields due to total removal of crop residues (Zambezi & Mwambula, 1997) for feed coupled with the high cost of fertilizers that restrict farmers to little (Mosier, Syers, & Freney, 2005) or no use of fertilizers. Therefore, developing and promoting maize varieties that are productive under low soil-N conditions is desirable. Although several Low-N-tolerant maize populations have been developed in the sub-region (Ajala, Olaniyan, Olayiwola, & Job, 2018), very few hybrids with tolerance to low-N have been specifically developed for the region, yet the use of hybrids is essential to attain appreciable increase in maize production and sustainable agriculture (MacRobert, 2009; Oyekunle & Badu-Apraku, 2013). Consequently, current maize breeding efforts for the region focuses on the development of Low-N-tolerant inbred

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Assessment of genetic diversity among low-nitrogen-tolerant early generation maize inbred lines using SNP markers

Cited by 17 publications

References 28 publications

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

Genetic diversity analysis of a flax (Linum usitatissimum L.) global collection

Genetic diversity analysis of a Flax (Linum usitatissimum L.) global collection

Assessment of heterotic patterns of tropical low‐nitrogen–tolerant maize (Zea maysL.) inbred lines using testcross performance, morphological traits and SNP markers

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