TY - JOUR
T1 - A first genetic map in the genus Streptocarpus generated with RAD sequencing based SNP markers
AU - Chen, Y. Y.
AU - Nishii, K.
AU - Barber, S.
AU - Hackett, C.
AU - Kidner, C. A.
AU - Gharbi, K.
AU - Nagano, A. J.
AU - Iwamoto, A.
AU - Möller, M.
N1 - Added retrospectively / All rights reserved / check with authors reason for not depositing on time / request AAM 20/05/2019 EN
PY - 2018/7/1
Y1 - 2018/7/1
N2 - Streptocarpus shows a great diversity of shoot and flower morphology, but lacks resources for genetic studies. RAD sequencing with NGS technologies provides large amounts of genotyping data quickly and cost effectively and is very useful for genetic map construction. In this study, three approaches for constructing RAD loci were combined to build the first genetic map for Streptocarpus (Gesneriaceae). A backcross population between Streptocarpus grandis and S. rexii was used as the mapping population. The parents are both diploid (2n = 32) and largely autogamous. Streptocarpus grandis is unifoliate, retaining the enlarged macrocotyledon as sole foliar organ which is monocarpic, and S. rexii is rosulate and perennial. 233 backcross plants were genotyped, and the data from 200 or 150 individuals used to generate the maps. The RAD reads were assembled using a de novo approach, aligned on the reference draft genome sequences of S. rexii using BWA or Stampy, and finally all markers were analyzed combined. In the latter, 599 mappable markers were generated which were assigned to 16 linkage groups, with an average inter-marker distance of 2.6 cM. This work provides a valuable genetic resource for further studies in the large and morphologically diverse genus Streptocarpus.
AB - Streptocarpus shows a great diversity of shoot and flower morphology, but lacks resources for genetic studies. RAD sequencing with NGS technologies provides large amounts of genotyping data quickly and cost effectively and is very useful for genetic map construction. In this study, three approaches for constructing RAD loci were combined to build the first genetic map for Streptocarpus (Gesneriaceae). A backcross population between Streptocarpus grandis and S. rexii was used as the mapping population. The parents are both diploid (2n = 32) and largely autogamous. Streptocarpus grandis is unifoliate, retaining the enlarged macrocotyledon as sole foliar organ which is monocarpic, and S. rexii is rosulate and perennial. 233 backcross plants were genotyped, and the data from 200 or 150 individuals used to generate the maps. The RAD reads were assembled using a de novo approach, aligned on the reference draft genome sequences of S. rexii using BWA or Stampy, and finally all markers were analyzed combined. In the latter, 599 mappable markers were generated which were assigned to 16 linkage groups, with an average inter-marker distance of 2.6 cM. This work provides a valuable genetic resource for further studies in the large and morphologically diverse genus Streptocarpus.
KW - Genetic linkage map
KW - Genome sequence
KW - Next generation sequencing
KW - RAD sequencing
KW - Streptocarpus grandis
KW - Streptocarpus rexii
UR - http://www.scopus.com/inward/record.url?scp=85047638708&partnerID=8YFLogxK
U2 - 10.1016/j.sajb.2018.05.009
DO - 10.1016/j.sajb.2018.05.009
M3 - Article
AN - SCOPUS:85047638708
VL - 117
SP - 158
EP - 168
JO - South african journal of botany
JF - South african journal of botany
SN - 0254-6299
ER -