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Table 4 Marker mining on 23 genome sequence assembly scaffolds bearing 24 markers linked to 11 key genes of agronomic traits of interest by sequence alignments among 10 sequenced cultivars of Lupinus angustifolius a

From: Application of whole genome re-sequencing data in the development of diagnostic DNA markers tightly linked to a disease-resistance locus for marker-assisted selection in lupin (Lupinus angustifolius)

Agronomic traits Name of markers Distance between marker and target gene (cM) Reference Scaffold identified Scaffold size (bp) Number of SNP markers from scaffold sequence alignment Number of InDel markers from scaffold sequence alignment
Disease resistance gene PhtjR DAFWA6895 0 [38] Scaffold84773 33,448 489 101
Disease resistance gene PhtjR PhtjM1 1.3 [44] scaffold70674 11,068 102 39
Disease resistance gene PhtjR PhtjM4 1.1 [44] scaffold16849 40,716 526 259
Disease resistance gene PhtjR PhtjM6 1.9 [44] scaffold2572 55,753 808 263
Disease resistance gene PhtjR PhtjM7 1.1 [44] scaffold57606 13,893 188 62
Disease resistance gene Lanr1 DAFWA5820 0 [38] scaffold 31581 15,706 225 33
Disease resistance gene Lanr1 AntjM1 3.5 [22] scaffold83350 11,407 74 35
Disease resistance gene Lanr1 AntjM2 2.3 [14] scaffold2992 33,979 341 188
Disease resistance gene Lanr1 AnSeq3 0.9 [37] Scaffold33942 64,039 716 138
Disease resistance gene Lanr1 AnSeq4 0.9 [37] Scaffold31346 33,727 221 158
Seed coat colour DAFWA6428 0 [38] scaffold11676 22,481 588 154
Seed coat colour DAFWA4544 0 [38] scaffold13708 44,176 821 81
Disease resistance gene AnMan AnManM1 5.0 [16] scaffold36514 50,220 311 213
Disease resistance gene Phr1 Ph258M1 5.7 [21] scaffold84752 21,471 292 94
Disease resistance gene Phr1 Ph258M2 2.1 [21] scaffold16252 15,559 212 25
Resistance gene against lupin rust disease RustM1 Unknown Unpublished scaffold15347 42,210 578 25
Early flowering gene Ku KuH 0 [25] scaffold21489 30,923 676 23
Soft-seed coat gene mollis MoA, MoLi 0 [23, 30] scaffold75616 14,783 63 16
Pod-non-shattering le LeLi 6.0 [29] scaffold87978 9,909 59 17
Pod-non-shattering gene le LeM2 1.3 [24] scaffold79908 20,738 103 22
Pod-non-shattering gene tardus TaM1 2.1 [26] scaffold15347 21,529 578 25
Pod-non-shattering gene tardus TaLi 1.4 [27] scaffold36274 8,191 62 4
Low alkaloid gene iucundus IucLi 0.9 [28] scaffold30160 20,677 667 22
Average scaffold size and marker numbers 27,687 378 87
  1. aThe list of 10 sequenced cultivars is presented in Tables 2 and 5