Validation of SSR Markers Linked to Flowering Time QTLs in Sorghum through Progeny Test

Flowering time is critically important for crop yield, and detection of its genetic factors with strongly associated DNA markers is necessary in breeding programs. This study was undertaken to validate the quantitative trait loci （QTLs） underlying flowering time of sorghum based on the association between genotypes at SSR marker loci and flowering time in F3 family lines from self-pollinated heterozygous F2 plants developed by crossing between ＂SC112＂---an early flowering variety from Ethiopia and ＂Kikuchi Zairai＂--a late flowering variety from Japan. The results showed that the SSR markers linked to the QTLs on sorghum chromosomes 1, 2, 3, 5b, 7 and 8b were significantly （P 〈 0.05） associated with flowering time, and these markers and the QTLs reported previously are valid. On the other hand, the genotypes at the marker locus SB596 of qFT1-2 on chromosome 1 was not significantly associated with flowering time. The valid DNA markers, SB258 in qFTI-1, SB 1512 in qFT2, SB 1839 in qFT3, SB3369 in qFT5b, SB4096 in qFT7 and SB4540 and SB4660 in qFT8b, might be useful for DNA-marker assisted breeding.

BSA-seq-based identification of a major additive plant height QTL with an effect equivalent to that of Semi-dwarf 1 in a large rice F_(2) population

Bulked-segregant analysis is a time-and cost-saving strategy for identifying major quantitative trait loci(QTL) in a mapping population. Bulked-segregant analysis combined with whole-genome sequencing(BSA-seq) was performed to rapidly identify QTL for heading date, plant height, and panicle length in a large F_(2) population derived from two landraces: Chuan 7(C7) and Haoboka(HBK). Twenty plants with extremely low or high phenotypic values for the target traits were selected from an F_(2) population of 940 plants to construct low-and high-value bulks. Three pairs of bulks for the three traits were constructed, resulting in six DNA pools. BSA-seq revealed nine QTL: four for heading date, three for plant height, and two for panicle length. These QTL were validated in a random F_(2) population or BC_(4)F_(2) populations. The major novel plant height QTL, qPH8, acting additively with an effect equivalent to that of semi-dwarf 1(sd1), is potentially valuable for hybrid rice breeding. qPH8 controls mainly the elongation of basal internodes. The C7 allele of qPH8 reduces plant height and increases lodging resistance without yield penalty, suggesting a potential role for qPH8 in improving rice plant architecture.

A major and stable QTL for wheat spikelet number per spike validated in different genetic backgrounds

The spikelet number per spike(SNS)contributes greatly to grain yield in wheat.Identifying various genes that control wheat SNS is vital for yield improvement.This study used a recombinant inbred line population genotyped by the Wheat55K single-nucleotide polymorphism array to identify two major and stably expressed quantitative trait loci(QTLs)for SNS.One of them(QSns.sau-2SY-2D.1)was reported previously,while the other(QSns.sau-2SY-7A)was newly detected and further analyzed in this study.QSns.sau-2SY-7A had a high LOD value ranging from 4.46 to 16.00 and explained 10.21-40.78%of the phenotypic variances.QSns.sau-2SY-7A was flanked by the markers AX-110518554 and AX-110094527 in a 4.75-cM interval on chromosome arm 7AL.The contributions and interactions of both major QTLs were further analyzed and discussed.The effect of QSns.sau-2SY-7A was successfully validated by developing a tightly linked kompetitive allele specific PCR marker in an F_(2:3) population and a panel of 101 high-generation breeding wheat lines.Furthermore,several genes including the previously reported WHEAT ORTHOLOG OF APO1(WAPO1),an ortholog of the rice gene ABERRANT PANICLE ORGANIZATION 1(APO1)related to SNS,were predicted in the interval of QSns.sau-2SY-7A.In summary,these results revealed the genetic basis of the multi-spikelet genotype of wheat line 20828 and will facilitate subsequent fine mapping and breeding utilization of the major QTLs.

A major vernalization-independent QTL for tiller angle on chromosome arm 2BL in bread wheat

Tiller angle(TA)strongly influences plant architecture and grain yield in cereals.However,the genetic basis of TA in wheat is largely unknown.We identified three TA-related quantitative trait loci(QTL).One of them was QTa.sau-2 B-769,a major QTL localized on chromosome arm 2 BL.QTa.sau-2 B-769 was detected in seven environments,explaining 18.1%–51.1%of phenotypic variance.We developed a linked Kompetitive Allele-Specific Polymerase chain reaction(KASP)marker,KASP-AX-108792274,to further validate this locus in three additional populations in multiple environments.QTa.sau-2 B-769 increased TA by up to 24.9%in these populations.There were significant and positive correlations between TA and flag leaf angle(FLANG).However,TA was not correlated with plant height or anthesis date,suggesting that expression of QTa.sau-2 B-769 is independent of vernalization.Traes CS2 B01 G583800,a gene known to be involved in leaf angle regulation,was identified as the most likely candidate gene for QTa.sau-2 B-769.These results enrich our understanding of the mechanisms regulating wheat TA at maturity and may support precise mapping and cloning of gene(s)underlying QTa.sau-2 B-769.

Additive and additive × additive interaction make important contributions to spikelets per panicle in rice near isogenic (Oryza sativa L.) lines

Epistasis plays an important role in the genetic basis of rice yield traits. Taking interactions into account in breeding programs will help the development of high-yielding rice varieties. In this study, three sets of near isogenic lines （NILs） targeting three QTLs for spikelets per panicle （SPP）, namely qSPP1, qSPP2 and qSPP7, which share the same Zhenshan 97 genetic background, were used to produce an F 2 population in which the three QTLs segregated simultaneously. The genotypes of the individual F 2 plants at the three QTLs were replaced with three markers that are closely linked to the corresponding QTLs. These QTLs were validated in the F 2 and F 3 populations at the single marker level. qSPP7 exhibited major pleiotropic effects on SPP, plant height and heading date. Multifactor analysis of variance was performed for the F 2 population and its progeny. Additive × additive interaction between qSPP2 and qSPP7 had significant effects on SPP in both the F 2 population and its progeny. Both additive and additive × additive interactions could explain about 73% of the total SPP phenotypic variance. The SPP performance of 27 three-locus combinations was ranked and favorable combinations were rec- ommended for rice breeding in different ecosystems.