Table 5.
Summary of the combinations used for clustering by MetaQTL
| RIL experimental site$ | BC$ | |||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chr | Trait | Total QTLs | Parent | Total clusters identified* | Meta - cluster designation | Clusters coalesced into Meta - clusters | cM | Ge6 | Cs7 | Mp7 | Br7 | Ga7 | Lu7 | Cs8 | Mp8 | Lu8 | Br8 | Cs9 | BC1 | BC2 | BC2S1 | Confirms litera - ture |
| 2 | Fineness | 18 | Gua | 3(+ 1) | FIN_2 | 1 + 2 + 3 | 23 + 36 - 43 | x | x | x | x | x | (x) | x | yes (# loc) | |||||||
| Elongation | 6 | Gua | 1 | ELO_2 | 1 | 46 | NA | NA | NA | NA | x | x | x | x | yes | |||||||
| 3 | Length | 26 | VH8 | 3(+ 1) | LEN_3 | 2 + 3 | 36 - 47 | x | x | x | (x) | (x) | x | x | x | yes | ||||||
| Strength | 9 | VH8 | 1(+ 3) | STR_3 | 4 | 110 | NA | x | x | x | x | x | (x) | (x) | yes | |||||||
| Fineness | 15 | VH8 | 3 | indicative | 3 | (101) | x | x | x | x | (x) | (x) | yes (# loc) | |||||||||
| 4 | Length | 9 | Gua | 1 | LEN_4 | 1 | 67 | x | x | x | x | x | x | yes | ||||||||
| 5 | Fineness | 11 | Gua | 4 | indicative | 1 + 2 + 3 | (25 - 45 - 50) | x | x | x | x | x | yes | |||||||||
| Length | 11 | Gua | 3(+ 1) | indicative | 1 + 2 + 3 | (22 - 32 - 49) | x | x | x | x | x | yes | ||||||||||
| 6 | Color | 13 | Gua | 3 | COL_6 | 3 | 35 - 45 - 51 | NA | x | x | x | x | NA | NA | x | NA | x | x | yes | |||
| 8 | Color | 34 | Gua | 7 | COL_8A | 2 + 3 + 4 | 46 - 51 - 54 | x | NA | x | x | x | NA | x | NA | NA | ||||||
| COL_8B | 5 + 6 + 7 + 8 | 84 - 88 - 109 - 121 | NA | x | NA | NA | x | NA | x | x | yes | |||||||||||
| 9 | Fineness | 25 | VH8 | 4(+ 3) | FIN_9A | 1 + 2 + 3 | 20 - 41 - 51 | x | x | x | x | x | x | |||||||||
| FIN_9B | 6 + 7 | 95 - 102 | x | x | x | yes | ||||||||||||||||
| Length | 8 | Gua | 3 | LEN_9 | 1 + 2 + 3 | 18 - 36 - 39 | x | x | x | x | yes (oppos) | |||||||||||
| 10 | Fineness | 16 | VH8 | 5(+ 1) | FIN_10 | 3 + 4 + 5 | 58 - 70 - 81 | x | x | x | x | (x) | x | yes | ||||||||
| 12 | Fineness | 20 | VH8 | 2(+ 4) | FIN_12 | 1 + 2 | 4 - 14 | (x) | x | (x) | (x) | x | x | x | x | x | yes | |||||
| 15 | Fineness | 30 | VH8 | 6 | FIN_15 | 2 + 3 + 4 + 5 | 62 - 67 - 73 - 84 | x | x | x | x | (x) | x | x | x | (x) | (x) | yes | ||||
| Elongation | 10 | Gua | 2(+ 2) | ELO_15 | 2 + 3 | 68 - 72 | NA | NA | NA | x | x | NA | x | x | (x) | yes | ||||||
| 16 | Fineness | 10 | VH8 | 6 | indicative | 1 + 2 + 3 | (41 - 50 - 64) | (x) | x | (x) | x | (x) | x | yes | ||||||||
| 17 | Fineness | 14 | VH8 | 2 | FIN_17 | 1 + 2 | 18 - 28 | x | x | x | x | x | x | yes | ||||||||
| 18 | Fineness | 17 | VH8 | 5 | FIN_18 | 3 | 49 | x | x | x | (x) | x | (x) | x | x | (x) | yes (oppos) | |||||
| 19 | Elongation | 14 | Gua | 5 | indicative | 1 + 2 + 3/4 + 5† | (83 - 148) | NA | NA | NA | x | x | NA | x | x | x | x | yes | ||||
| Length | 15 | Gua | 5 | indicative | 2 + 3 + 4 | (64 - 101) | x | x | x | x | x | yes (oppos) | ||||||||||
| Fineness | 18 | Gua | 7 | indicative | 2 + 3 + 4 + 5/6 + 7† | (51 - 200) | x | x | x | x | x | x | x | x | yes (oppos) | |||||||
| 21 | Strength | 7 | VH8 | 2(+ 2) | STR_21 | 2 + 3 | 75 - 80 | (x) | NA | (x) | (x) | x | x | x | yes | |||||||
| Fineness | 23 | VH8 | 7 + 1 | FIN_21A | 2 + 3 + 4 + 5 | 65 - 73 - 81 - 93 | x | x | x | x | x | x | x | yes | ||||||||
| FIN_21B | 6 + 7 + 8 | 129 - 149 - 163 | x | x | x | x | x | x | x | yes | ||||||||||||
| 23 | Length | 10 | VH8 | 2 + 1 | LEN_23 | 2 + 3 | 98 - 117 | x | (x) | x | x | x | x | yes (# loc) | ||||||||
| Strength | 9 | VH8 | 2(+ 2) | indicative | 3 + 4 | (86 - 102) | NA | x | x | x | yes | |||||||||||
| 24 | Length | 7 | VH8 | 1(+ 1) | LEN_24 | 1 + 2 | 67 - 75 | x | x | x | x | yes (# loc) | ||||||||||
| 25 | Color | 25 | Gua | 5(+ 1) | COL_25A | 1 + 2 + 3 | 46 - 57 - 66 | NA | x | x | x | NA | NA | x | NA | x | x | x | yes | |||
| COL_25B | 4 + 5 | 80 - 84 | NA | x | x | x | x | NA | NA | NA | x | |||||||||||
| Fineness | 25 | VH8 | 5 | FIN_25 | 2 | 48 - 60 | x | (x) | x | x | x | x | x | yes | ||||||||
| 26 | Length | 16 | Gua | 5 | indicative | 1 + 2/3/4 + 5† | (8 to 94) | x | x | x | x | x | x | yes (oppos) | ||||||||
* the 1st number represents the number of "reliable" clusters supported by QTLs from multiple experimental sites. Additional clusters represented by isolated QTLs are shown in parentheses
$ x, indicates that meta-cluster was supported by QTL detected at this experimental site, (x) that isolated QTLs was observed, NA that the trait was not measured
† the slash separates groups of clusters suspected to delineate different indicative meta-clusters
Summary of the 30 trait x chromosome combinations used for clustering by MetaQTL software and of 25 highly supported meta-clusters. Total of QTLs (LOD>2) detected, shared direction of additivity (toward Guazuncho-2 (GUA), G. hirsutum, or VH8-4602 (VH8), G. barbadense, parent), number of clusters in best clustering model as proposed by MetaQTL (following Akaike-information criterion), names and positions of highly supported clusters and meta-clusters, and indication for an occurrence of at least one congruence (same region and same directionality Gh/Gb) with QTL reported in the literature. Meta-cluster designation (trait acronym and chromosome) is suffixed with a letter (A, B) when several meta-cluster are mapped on the same chromosome.