Optimizing sample size for molecular characterization of open-pollinated maize (Zea mays L.) varieties using simple sequence repeat markers

Molecular-based characterization of open-pollinated varieties (OPVs) in maize is useful to define their unique profiles. A total of 58 SSR markers selected from a panel of 70 were used for genotyping three samples of 30, 50 and 100 plant bulks for each of 32 OPVs. The SSR markers detected a total of 253 alleles in the 32 maize OPVs across the three bulk samples. The number of alleles per marker varied from 2 to 7, with an overall mean of 4.36. The genetic distance among the OPVs varied from 0.17 to 0.93 with an average of 0.70 ± 0.007 for bulk samples of 30 plants, 0.20 to 0.91 with an overall mean of 0.70 ± 0.007 for bulk samples of 50 plants and from 0.30 to 0.95 with an average of 0.75 ± 0.006 for bulk samples of 100 plants. Cluster analysis separated the 32 maize OPVs into two major groups, which were further separated into two sub-groups for each type of bulk sample. The groupings of the OPVs into two major groups and their corresponding sub-groups was consistent with known breeding history (common parentage) and common target traits during development of the OPVs irrespective of the sample size used. However, in the bulk samples of 50 and 100 plants, some sub-groups were composed of OPVs with mixed maturity classes and diverse genetic backgrounds. Of the three independent bulk samples, the smallest sample size of 30 plants was found to be optimal for characterizing heterogeneous and heterozygous maize populations and OPVs owing to its cost-effectiveness and relative ease of sample processing

Performance of tropical maize hybrids under conditions of low and optimum levels of nitrogen fertilizer application grain yield, biomass production and nitrogen accumulation

Nitrogen (N) is the most limiting mineral nutrient in the soils of the major maize producing areas of West and Central Africa. Low soil N and sub-optimal application of N fertilizers lead to N deficiency and poor grain yield (GY) in maize. Maize varieties with improved grain yield under low soil N and increased performance under optimal N availability could be beneficial to low input agriculture. This study evaluated the performance of a selection of experimental and commercial hybrids under suboptimal and optimal N fertilizer applications. Significant differences were observed among the hybrids, as well as significant interactions between hybrid and N level for GY and other measured attributes, with the severity of variation increasing as the level of N decreases. Mean GY reductions across the years was 76.5% at no-N and 35.4% at low-N. Depending on N treatment, GY varied from 0.48 to 4.42 Mg ha-1, grain N content from 0.17 to 1.26 g plant-1, total N content at harvest from 0.33 to 2.00 g plant-1, above ground biomass at silking from 30.6 to 91.2 g plant-1 and at maturity from 39.9 to 191.1 g plant-1. Number of kernels was the GY component most severely reduced by N stress and had significant (p = 0.001) positive correlation with GY at all N levels. Six hybrids (4001/4008, KU1409/4008, KU1409/9613, 4008/1808, 4058/Fun 47-4, and 1824/9432) which showed consistent above average grain yields under no-N, low-N, high-N and across N levels were found and their use could further be investigated

Diversity Analysis of Elite Maize Inbred Lines Adapted to West and Central Africa Using SSR Markers

Seventeen elite maize inbred lines of West and Central Africa adaptation with tropical and temperate x tropical origin were investigated for diversity at 18 SSR loci in non-coding regions of the maize genome, alongside two temperate inbred lines (B73 and Mo17), perennial teosinte (Zea diploperennis) and gamagrass (Tripsacum dactyloides). A total of 174 alleles were detected with a range of 5 to 15 alleles per maker and an average of 9.7 alleles per locus. Polymorphic information content (PIC) ranged from 0.29 in umc1226 to 0.92 in bnlg2122 with an average of 0.75. Relationships between heterotic groups and groups based on SSR data were quite varied for the lines studied. Primarily, the SSR markers grouped the lines on the basis of their origin, with three instances of a pair of heterotic lines clustering together; one pair of temperate origin and the other two tropical vs temperate x tropical. Four inbred lines (CMR 19, CMR 20, CMR 21, and CMR 26), belonging to three heterotic groups were, however, differentiated by SSR data. The markers showed potential for use in managing inbred lines germplasm adapted to West and Central Africa, particularly for classifying inbred lines for which records of ancestry are not readily available and for exploiting the heterosis known for tropical vs. temperate x tropical crosses

Validation of diagnostic markers for streak virus disease resistance in maize

Open Access Journal; Published online: 05 Feb 2021Maize streak virus (MSV) is responsible for streak disease of maize and poses a serious threat to maize production in sub-Saharan Africa. Polygenic resistance to MSV has become an essential requirement in modern maize cultivars to mitigate yield losses. Many single nucleotide polymorphism (SNP) markers linked to putative MSV resistance loci have been identified for use in forward breeding. This study aimed to validate, using the high-throughput kompetitive allele specific PCR (KASP) assay, the diagnostic ability of the three SNP markers linked to the loci for the Msv1 resistance trait in 151 early generations inbred lines with diverse genetic backgrounds, together with nine MSV-resistant elite lines and a susceptible check (cv. Pool-16). The phenotypic responses were determined by MSV inoculation using viruliferous leafhoppers (Cicadulina triangular) under screenhouse conditions. Based on an established MSV disease rating system, the maize lines were categorized into resistant, moderately resistant, susceptible, and highly susceptible. The three SNPs associated with MSV resistance were detected in 133 lines, which were categorized as resistant (54), moderately resistant (76), and susceptible (1). The 18 early generation lines without these SNPs were classified as moderately resistant (10), susceptible (5), and highly susceptible (3). This study confirms the strong association of SNPs with MSV resistance and their usefulness for forward breeding in maize while emphasizing the need to identify additional markers to screen lines for MSV resistance without any ambiguity

Effectiveness of yellow maize testers with varying resistance reactions to Striga hermonthica for evaluating the combining ability of maize inbred lines

Open Access Journal; Published online: 28 Aug 2020The choice of an appropriate tester is important for success in resistance hybrid breeding programs. Limited information is available on the most suitable testers that allow the selection of yellow endosperm maize inbred lines with good combining ability for resistance to witchweed (Striga hermonthica) and superior agronomic performance in hybrids targeted to areas infested with the parasite. Testcrosses of 30 Striga-resistant yellow endosperm maize inbred lines with three testers having varying levels of resistance to S. hermonthica were evaluated at Abuja and Mokwa in Nigeria under Striga-infested and non-infested conditions in 2018 and 2019. The lines × tester interaction was significant for grain yield under Striga infestation, indicating that the performance lines in testcrosses varied with the testers. The respective average general combining ability effect of lines and testers was 1.5 and 32.4 times greater than the corresponding specific combining ability effects under infestation, showing the greater importance of additive gene action controlling the performance of testcrosses under Striga infestation. The different testers exhibited a different capacity to discriminate among the test lines with the susceptible tester being the least effective. Most of the criteria used to determine the best tester favored the selection of the tolerant and resistant testers as promising candidates to identify superior Striga-resistant yellow endosperm inbred lines for the hybridization and development of resistant hybrids. The results of this study demonstrated that testers with a high frequency of desirable alleles were superior to the tester with a low frequency of favorable alleles in hybrid breeding programs for resistance to S. hermonthica

Identifying suitable tester for evaluating Striga resistant lines using DArTseq markers and agronomic traits

Open Access Journal; Published online: 18 June 2021A desirable tester that elicits greater genetic difference in Striga resistance among test crosses in a breeding program has not been reported. Therefore, this study was conducted to characterize 30 Striga resistant yellow endosperm maize inbred lines and three testers with varying resistance levels to Striga using DArTseq SNP markers and agronomic traits to identify a suitable tester for resistance hybrid breeding. Marker-based and agronomic trait-based genetic distances were estimated for yellow endosperm maize inbred lines and testers with varying resistance levels to Striga. The Marker-based cluster analysis separated the Striga resistant lines and testers into two distinct groups. Although the susceptible tester (T3) was the most distantly related to the 30 Striga resistant inbred lines, it exhibited a narrower range in genetic distance estimates and poor agronomic performance under Striga infestation in crosses with the resistant lines. In contrast, the resistant tester (T2) showed a broader range in genetic distance estimates in pairs with the 30 resistant lines. Also, it formed many high yielding hybrids with desirable traits under parasite pressure. Furthermore, the most significant positive association between agronomic trait-based and marker-based distance estimates (r = 0.389, P = 0.01) was observed when T2 has paired with the Striga resistant maize inbred lines. It thus appears that T2 may be used as a suitable tester to determine the breeding value of lines in hybrid maize resistance breeding programs. T2 was the most suitable tester, with a tolerant tester (T1) as an alternative tester to characterize the combining ability of Striga resistant maize inbred lines. This result can also encourage other breeders to investigate testers relative discriminating ability with varying levels of resistance in hybrid breeding for resistance to diseases, pests, and other parasitic plants

Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.)

Published online: 31 Jul 2020Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam

Suitability of testers to characterize provitamin a content and agronomic performance of tropical maize inbred lines

Open Access Journal; Published online: 08 Aug 2022Vitamin A deficiency poses health risks for children, pregnant women, and nursing mothers in sub-Saharan Africa (SSA) and Southeast Asia. Provitamin A–biofortified maize varieties can contribute to minimizing the adverse effects of vitamin A deficiency in areas where maize is a staple food crop. Identifying suitable testers is important to breed provitamin A–biofortified hybrid maize. This study was therefore conducted to 1) assess the suitability of maize inbred lines with contrasting levels of provitamin A (one with high and one with low provitamin A concentration) to assess the combining ability of maize inbred lines in accumulating provitamin A and other carotenoids, and grain yield, 2) confirm the mode of inheritance of provitamin A and grain yield, and 3) identify promising inbred lines with desirable combining ability effects for use to develop high-yielding provitamin A–biofortified hybrids. The inbreds crossed to the two inbred testers were evaluated in four environments for the carotenoid content and eight environments for the agronomic performance. The combined analysis of variance revealed a significant genetic variation among the testcrosses for all carotenoids, grain yield, and other agronomic traits. The mode of inheritance for grain yield, other agronomic traits, provitamin A, and other carotenoids was regulated by both additive and non-additive gene effects with a prominence of additive gene effects. The high provitamin A tester that displayed positive GCA effects for β-carotene and provitamin A content, broader agronomic performance of testcrosses, and higher levels of provitamin A in testcrosses can be considered suitable for breeding programs developing provitamin A–biofortified hybrids. The inbred lines TZI2012, TZI2142, TZI2130, TZI2065-2, TZI2161, TZI2025, TZI1278, TZI1314, TZI1304, and TZI2032 with positive GCA effects for grain yield and provitamin A content could be used as parental lines to develop source population of new inbred lines and high-yielding hybrids with elevated levels of provitamin A. The best performing hybrids are promising for release as highyielding provitamin A maize hybrids after further evaluations

Comparative assessment of effectiveness of alternative genotyping assays for characterizing carotenoids accumulation in tropical maize inbred lines

Open Access Journal; Published online: 09 Oct 2021The development of maize varieties with increased concentration of Provitamin A (PVA) is an effective and affordable strategy to combat vitamin A deficiency in developing nations. However, the considerably high cost of carotene analysis poses a major challenge for maize PVA biofortification, prompting the use of marker-assisted selection. Presently, two types of genotyping with PVA trait-linked functional markers have been developed and extensively used in breeding programs. The two systems are low throughput gel-based genotyping and genotyping with Kompetitive Allele-Specific PCR (KASP) single nucleotide polymorphism (SNPs) markers. Although the KASP SNPs genotyping was developed to replace the gel-based genotyping, studies have not been conducted to compare the effectiveness of the KASP SNPs markers with the gel-based markers. This study was conducted to assess the carotenoid content of 64 tropical PVA biofortified maize inbred lines containing temperate germplasm in their genetic backgrounds and screen them with both gel-based and KASP markers of PSY1, LCYE and crtRB1 genes. Many of the 64 inbred lines had PVA concentrations surpassing the 15 µg/g provitamin A breeding target set by the HarvestPlus Challenge Program. Favorable alleles of crtRB1, crtRB1 and the KASP SNPs markers were detected in 25 inbred lines with high PVA concentrations. Inbred lines with the favorable alleles of LCYE had the highest concentrations of non-PVA carotenoids, whereas those with the favorable alleles of crtRB1 had high levels of PVA carotenoids. Data from the sequenced region of LCYE revealed one SNP in the first intron that clearly differentiated the high and low β-carotene maize inbred lines. The results of our study demonstrate that the automated KASP SNPs markers can replace the gel-based genotyping for screening a large number of early generation maize inbred lines for PVA content

Inheritance of Striga hermonthica adaptive traits in an earlymaturing white maize inbred line containing resistance genes from Zea diploperennis

Striga hermonthica can cause as high as 100% yield loss in maize depending on soil fertility level, type of genotype, severity of infestation and climatic conditions. Understanding the mode of inheritance of Striga resistance in maize is crucial for introgression of resistance genes into tropical germplasm and deployment of resistant varieties. This study examined the mode of inheritance of resistance to Striga in early‐maturing inbred line, TZdEI 352 containing resistance genes from Zea diploperennis. Six generations, P1, P2, F1, F2, BC1P1 and BC1P2 derived from a cross between resistant line, TZdEI 352 and susceptible line, TZdEI 425 were screened under artificial Striga infestation at Mokwa and Abuja, Nigeria, 2015. Additive‐dominance model was adequate in describing observed variations in the number of emerged Striga plants among the population; hence, digenic epistatic model was adopted for Striga damage. Dominance effects were higher than the additive effects for the number of emerged Striga plants at both locations signifying that non‐additive gene action conditioned inheritance of Striga resistance. Inbred TZdEI 352 could serve as invaluable parent for hybrid development in Striga endemic agro‐ecologies of sub‐Saharan Africa