2.2. QTL Mapping in Five DH Populations
A total map length of 3688.3, 4004.6, 3871.9, 7193.1, and 3426.4 cM was obtained from 2104, 2699, 1962, 1985, and 2086 SNP markers (Table 1
) for populations 1, 2, 3, 4, and 5, respectively. The average distance between adjacent markers ranged from 1.48 cM for population 2 to 3.62 cM for population 4.
QTL analysis identified 155 significant QTL for GY, AD, ASI, PH, EH, EPO, and SEN across ten maize chromosomes under optimum (55), LNM (49), and LNO (51) conditions (Table 2
). Though slightly higher under optimum conditions, the total number of QTL identified for all N conditions, traits, and populations were comparable. The total number of QTL identified for GY, AD, ASI, PH, EH, EPO, and SEN were 13, 43, 13, 25, 30, 21, and 10, respectively. The distribution of QTL was variable among chromosomes, ranging between 6 (chromosome 9) and 51 (chromosome 1), with an average of 15.5 QTL in each chromosome. The three chromosomes with the largest number of QTL were chromosome 1 (51), chromosome 3 (26), and chromosome 8 (20). The distribution of the QTL across the five populations was 28, 84, 16, 13, and 14 for population 1, 2, 3, 4, and 5, respectively.
For GY, 13 significant QTL were identified under optimum (3), LNM (2), and LNO (8) conditions across all chromosomes, except chromosomes 5, 6, and 9 (Table 3
). Common QTL for optimum and low-N stressed conditions were not identified in all five populations. QTL underlying GY under optimum, LNM, and LNO conditions were identified on chromosomes 1, 2, 7, and 10 of population 2. About 62% of all QTL for GY individually contributed more than 10% of the observed phenotypic variance. The proportion of phenotypic variance explained by each QTL varied between 6.05 and 17.55%, with an average of 10.79%. The total phenotypic variance explained (TPVE) by all QTL under optimum conditions was 16.68% for population 1, 39.17% for population 2, and 9.32% for population 5. QTL for LNM were found only in population 2, and the TPVE was 11.50%.
The TPVE under LNO was 11.50% for population 2, 23.34% for population 3, 22.30% for population 4, and 30.54% for population 5. The average QTL effect size under optimum (0.14 t ha−1) conditions was the highest compared to LNM (0.04 t ha−1) or LNO (0.08 t ha−1) conditions. Interestingly, the favorable alleles of the QTL detected under all management conditions were contributed by both low-N tolerant and susceptible parents.
Forty-three significant QTL were identified for AD under optimum and low-N stressed conditions (Table 4
and Supplementary Table S1
) across all chromosomes and populations. The number of QTL identified was 18 under optimum, 13 under LNM, and 12 under LNO conditions. The largest number of QTL was detected in population 2 (16), followed by population 1 (15). The phenotypic variance explained by each QTL ranged between 3.19% and 95.81%, with an average of 17.40%. The total proportion of phenotypic variance explained by all QTL under optimum conditions was 71.31% for population 1, 46.88% for population 2, 29.02% for population 3 (only one QTL), and 13.36% for population 4 (only one QTL). Under LNM, TPVE was 28.86% for population 1, 58.04% for population 2, 12.04% for population 3 (only one QTL), 8% for population 4 (only one QTL), and 37.71% for population 5. The TPVE under LNO was 47.27% for population 1, 33.58% for population 2, 46.11% for population 3, 25.45% for population 4, and 29.69% for population 5. The effect size of all QTL ranged from 0.11 to 3.56 days, with an average of 0.54 days. Despite many (24) individual QTL explaining more than 10% phenotypic variance under different management conditions, only one QTL with high effect size under all management conditions was found. This QTL was identified on chromosome 1 (343 cM) from population 3. The effect size of this QTL was 2.99 days under optimum, 2.23 days under LNM condition, and 3.56 days under LNO condition. ASI is another secondary trait related to flowering and indicates the tolerance of maize genotypes to low-N stress. Only three QTL, one in population 2, 4, and 5, which explained more than 10% of phenotypic variation for ASI (Table 4
and Supplementary Table S2
) were identified. The TPVE by two QTL (39.41%) in population 5 was the highest attained in this study. The highest effect size for ASI was attained by these two QTL (0.53 and 0.32 days). Generally, the effect size for ASI varied between 0.05 and 0.53, days with an average of 0.14 days.
From the total of 25 QTL identified for PH from all populations on all chromosomes except chromosomes 4, 5, and 10, seven were under optimum, 10 under LNM, and eight under LNO conditions (Table 4
and Supplementary Table S3
). Only population 2 had QTL for all three management conditions. Thirteen QTL from the three conditions individually explained more than 10% phenotypic variance for PH. For the QTL in population 2, the TPVE was 59.82% under optimum, 61.72% under LNM, and 49.52% under LNO conditions. For populations 1 and 3, the total phenotypic variance explained by all QTL under LNM were 20.40% (one QTL) and 44.52%, respectively. Three QTL together explained 26.45% of the phenotypic variation observed for PH in population 1. One QTL each in population 3, 4, and 5 explained 24.33%, 8.05%, and 13.39% of the observed phenotypic variance for PH. The effect size of the individual QTL for PH ranged from 0.87 to 8.34 cm, with an average of 2.19 cm. Like AD, a QTL on chromosome 1 (343 cM) of population 3 combined more than 10% phenotypic variance and the highest effect size for PH. Two other QTL on chromosomes 1 (194.94 to 195.75 Mbp) and 8 (92.20 to 94.58 Mbp) of population 2 explained high phenotypic variance (16.96% and 13.92%) and had high effect size (3.27 and 2.99 cm). Like PH, the largest number of QTL for EH and EPO (Table 4
and Supplementary Tables S4 and S5
) was identified from population 2. The QTL on chromosome 1 of population 3, which combines a higher proportion of phenotypic variance explained and high QTL effect for AD and PH, also had the same effect for EH.
Unlike other traits in this study, QTL for SEN were identified only from population 2, with the largest number being under LNO (Table 4
and Supplementary Table S6
). The total phenotypic variance explained under optimum, LNM, and LNO conditions was 23.65%, 15.06%, and 45.87%, respectively. The highest amount of phenotypic variance and largest number of QTL under LNO indicates the genetic variability existing under LNO for SEN and the contrasting nature of the two parents that constituted population 2.